Variant report

Variant	rs12283300
Chromosome Location	chr11:71498601-71498602
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3442224..3443750-chr11:71497854..71499382,2	MCF-7	breast:
2	chr11:71498143..71498944-chr16:5147397..5148064,2	Hela-S3	cervix:
3	chr11:71498107..71498639-chr3:75483883..75484386,2	Hela-S3	cervix:
4	chr11:67572484..67573077-chr11:71498421..71498985,2	HCT-116	colon:
5	chr11:71498340..71499087-chr19:18391666..18392636,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000130522	Chromatin interaction
ENSG00000160172	Chromatin interaction
ENSG00000118894	Chromatin interaction
ENSG00000166492	Chromatin interaction
ENSG00000244026	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10898562	0.81[AMR][1000 genomes]
rs11234942	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11234943	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11234944	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12270466	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12277291	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12283346	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12418197	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12418483	0.80[AFR][1000 genomes]
rs12786196	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12786239	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12788252	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12788471	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12793051	0.82[AFR][1000 genomes]
rs2040301	0.82[AFR][1000 genomes]
rs3931640	0.80[AFR][1000 genomes]
rs4081496	0.80[AMR][1000 genomes]
rs4081498	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4944191	0.80[AMR][1000 genomes]
rs7111030	0.80[AFR][1000 genomes]
rs7112161	0.82[AFR][1000 genomes]
rs7112165	0.82[AFR][1000 genomes]
rs7123939	0.81[AMR][1000 genomes]
rs9326464	0.81[AFR][1000 genomes]
rs9666153	0.82[AFR][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	esv3379456	chr11:71496804-71499952	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
35	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12283300	FAM86C1	cis	Adipose Subcutaneous	GTEx
rs12283300	FAM86C1	cis	Muscle Skeletal	GTEx
rs12283300	FAM86C1	cis	Skin Sun Exposed Lower leg	GTEx
rs12283300	ALG1L9P	cis	Muscle Skeletal	GTEx
rs12283300	FAM86C1	cis	Artery Aorta	GTEx
rs12283300	FAM86C1	cis	Whole Blood	GTEx
rs12283300	CTD-2313N18.5	cis	Muscle Skeletal	GTEx
rs12283300	FAM86C1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71496800-71499200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr11:71497000-71499400	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr11:71497200-71498800	Active TSS	Fetal Muscle Leg	muscle
4	chr11:71497200-71498800	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr11:71497200-71498800	Active TSS	NH-A	brain
6	chr11:71497200-71499000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:71497200-71499000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:71497200-71499000	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr11:71497200-71499000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:71497200-71499000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:71497200-71499000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:71497200-71499000	Active TSS	Duodenum Mucosa	Duodenum
13	chr11:71497200-71499000	Active TSS	Fetal Brain Female	brain
14	chr11:71497200-71499000	Active TSS	NHEK	skin
15	chr11:71497200-71499200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:71497200-71499200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:71497200-71499200	Active TSS	Brain Anterior Caudate	brain
18	chr11:71497200-71499200	Active TSS	Brain Cingulate Gyrus	brain
19	chr11:71497200-71499200	Active TSS	Fetal Lung	lung
20	chr11:71497200-71499200	Active TSS	Thymus	Thymus
21	chr11:71497200-71499400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr11:71497200-71499400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:71497200-71499400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr11:71497200-71499400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr11:71497200-71499400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr11:71497200-71499400	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr11:71497200-71499400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:71497200-71499400	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr11:71497200-71499400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:71497200-71499400	Active TSS	Rectal Smooth Muscle	rectum
31	chr11:71497200-71499400	Active TSS	A549	lung
32	chr11:71497200-71499600	Active TSS	H1 Cell Line	embryonic stem cell
33	chr11:71497200-71499600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:71497200-71499600	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr11:71497200-71499600	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr11:71497200-71499600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:71497200-71499600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:71497200-71499600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:71497200-71499600	Active TSS	HepG2	liver
40	chr11:71497200-71499800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:71497400-71498800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:71497400-71498800	Active TSS	Placenta Amnion	Placenta Amnion
43	chr11:71497400-71499000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:71497400-71499000	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr11:71497400-71499000	Active TSS	Aorta	Aorta
46	chr11:71497400-71499000	Active TSS	Liver	Liver
47	chr11:71497400-71499000	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr11:71497400-71499000	Active TSS	Fetal Stomach	stomach
49	chr11:71497400-71499000	Active TSS	Ovary	ovary
50	chr11:71497400-71499000	Active TSS	Pancreas	Pancrea

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