Variant report

Variant	rs12801684
Chromosome Location	chr11:71506121-71506122
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10751157	0.87[CHB][hapmap]
rs10751166	0.87[CEU][hapmap];0.87[CHB][hapmap]
rs10792914	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10792915	0.80[ASN][1000 genomes]
rs10792951	0.84[AMR][1000 genomes]
rs10898585	0.83[CEU][hapmap];0.94[JPT][hapmap]
rs10898614	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10898618	0.90[AMR][1000 genomes]
rs10898623	0.80[ASN][1000 genomes]
rs11234944	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs11234970	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11235020	0.80[ASN][1000 genomes]
rs11235021	0.81[ASN][1000 genomes]
rs11606005	0.83[AMR][1000 genomes]
rs1814923	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2003240	0.83[AMR][1000 genomes]
rs2040301	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs3933397	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4021274	0.87[CEU][hapmap];0.87[CHB][hapmap]
rs4080976	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4945254	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4945263	0.82[AMR][1000 genomes]
rs61889010	0.81[ASN][1000 genomes]
rs6592327	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592335	0.91[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6592358	0.81[AMR][1000 genomes]
rs6592380	0.80[AMR][1000 genomes]
rs7111079	0.81[AFR][1000 genomes]
rs7117703	0.82[AFR][1000 genomes]
rs7127938	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7129769	0.91[CHB][hapmap]
rs7929123	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9326462	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9326465	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9666765	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9734986	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9736266	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9736964	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9888251	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv1037088	chr11:71293875-71538991	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv3527986	chr11:71298409-71620955	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv3527987	chr11:71298409-71620955	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1036258	chr11:71299175-71523551	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1041027	chr11:71299175-71527896	Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1051879	chr11:71299175-71536860	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv1044041	chr11:71299175-71538991	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	esv2761682	chr11:71299175-71619923	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv897903	chr11:71316093-71523766	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv897904	chr11:71316093-71615727	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv1035306	chr11:71326941-71523551	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv972041	chr11:71330518-71615123	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
14	esv1808002	chr11:71330564-71522967	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv832205	chr11:71336700-71523817	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	esv3369013	chr11:71338874-71612242	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv1054575	chr11:71352127-71536860	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv1047568	chr11:71352127-71538991	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	nsv1047177	chr11:71360190-71513585	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv427893	chr11:71363639-71529688	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	esv2758276	chr11:71363639-71657576	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
22	esv2759836	chr11:71363639-71657576	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
23	nsv428262	chr11:71363639-71804055	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
24	nsv1049480	chr11:71363999-71533919	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
25	nsv897905	chr11:71371354-71615727	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
26	esv1819073	chr11:71371742-71618164	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
27	nsv1044072	chr11:71379653-71527699	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
28	nsv1038551	chr11:71379653-71533919	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	nsv897906	chr11:71386905-71543708	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
30	nsv897907	chr11:71386905-71549174	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
31	nsv1045511	chr11:71395657-71527896	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
32	nsv1043197	chr11:71423465-71527699	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
33	nsv1037092	chr11:71443870-71527699	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
34	nsv482161	chr11:71498557-71512280	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
35	esv11723	chr11:71498860-71553549	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12801684	FAM86C1	cis	Artery Tibial	GTEx
rs12801684	FAM86C1	cis	Whole Blood	GTEx
rs12801684	FAM86C1	cis	Muscle Skeletal	GTEx
rs12801684	CTD-2313N18.5	cis	Nerve Tibial	GTEx
rs12801684	FAM86C1	cis	Skin Sun Exposed Lower leg	GTEx
rs12801684	FAM86C1	cis	Adipose Subcutaneous	GTEx
rs12801684	CTD-2313N18.5	cis	Artery Tibial	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71499000-71509600	Weak transcription	Ovary	ovary
2	chr11:71499000-71510600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:71499200-71507400	Weak transcription	Pancreas	Pancrea
4	chr11:71499200-71507800	Weak transcription	Esophagus	oesophagus
5	chr11:71499200-71510800	Weak transcription	Gastric	stomach
6	chr11:71499200-71511200	Weak transcription	Primary T cells from cord blood	blood
7	chr11:71499200-71511400	Weak transcription	Brain Angular Gyrus	brain
8	chr11:71499200-71511400	Weak transcription	Brain Anterior Caudate	brain
9	chr11:71499200-71511400	Weak transcription	Brain Hippocampus Middle	brain
10	chr11:71499200-71511400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:71499200-71515200	Weak transcription	Lung	lung
12	chr11:71499400-71508400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:71499400-71510400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:71499400-71510600	Weak transcription	Liver	Liver
15	chr11:71499400-71511000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr11:71499400-71511000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:71499400-71511200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:71499400-71511200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:71499400-71512000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:71499400-71512800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:71499400-71515200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:71499400-71515600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:71499600-71511400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr11:71499800-71506600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:71499800-71508200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:71499800-71511200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:71499800-71511400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:71499800-71512800	Weak transcription	Fetal Muscle Leg	muscle
29	chr11:71499800-71515200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr11:71500000-71510400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:71500000-71511200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:71500400-71507200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:71500400-71508600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:71500400-71511400	Weak transcription	A549	lung
35	chr11:71500400-71511400	Weak transcription	K562	blood
36	chr11:71500400-71515200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:71500400-71515200	Weak transcription	Fetal Intestine Large	intestine
38	chr11:71500400-71515600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr11:71500600-71506200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr11:71500800-71508800	Weak transcription	HepG2	liver
41	chr11:71500800-71515200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr11:71501200-71508800	Strong transcription	Fetal Intestine Small	intestine
43	chr11:71504000-71506600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr11:71504000-71506600	Enhancers	HSMM	muscle
45	chr11:71504000-71508400	Enhancers	HMEC	breast
46	chr11:71504600-71506200	Enhancers	Hela-S3	cervix
47	chr11:71505000-71506600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:71505000-71506800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:71505000-71507400	Enhancers	Placenta	Placenta
50	chr11:71505200-71506200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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