Variant report

Variant	rs11683487
Chromosome Location	chr2:152142549-152142550
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152132818..152134386-chr2:152140305..152143217,3	K562	blood:
2	chr2:152142404..152144724-chr2:152266453..152268489,2	K562	blood:
3	chr2:152140110..152142929-chr2:152143341..152145563,3	MCF-7	breast:
4	chr2:152124835..152127070-chr2:152140941..152143645,2	K562	blood:
5	chr2:152103117..152105386-chr2:152140432..152142822,2	K562	blood:

Variant related genes	Relation type
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10165186	0.86[EUR][1000 genomes]
rs10165284	0.86[EUR][1000 genomes]
rs10169816	0.83[JPT][hapmap]
rs10184314	0.87[EUR][1000 genomes]
rs10201139	0.86[EUR][1000 genomes]
rs10203366	0.87[EUR][1000 genomes]
rs10207408	0.86[EUR][1000 genomes]
rs10209942	0.86[EUR][1000 genomes]
rs10210155	0.86[EUR][1000 genomes]
rs1023635	0.80[EUR][1000 genomes]
rs1040234	1.00[YRI][hapmap]
rs1040235	1.00[YRI][hapmap]
rs1048135	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678123	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11678951	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11680338	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11691055	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11691217	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467046	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12469634	1.00[YRI][hapmap]
rs12471191	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12476687	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12624156	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12693004	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12987765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12996459	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12998170	0.87[EUR][1000 genomes]
rs13001328	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13004590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13007728	0.88[EUR][1000 genomes]
rs13015862	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13020769	0.87[EUR][1000 genomes]
rs13020962	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13025888	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13027425	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13030194	0.86[EUR][1000 genomes]
rs13412131	0.86[EUR][1000 genomes]
rs13420739	0.87[EUR][1000 genomes]
rs17796622	1.00[YRI][hapmap]
rs17798290	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2113508	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2194492	0.87[EUR][1000 genomes]
rs2218880	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271811	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278090	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28416443	0.84[EUR][1000 genomes]
rs2880488	0.87[ASN][1000 genomes]
rs289829	0.86[CHB][hapmap]
rs289906	0.81[EUR][1000 genomes]
rs289923	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs289924	0.82[AMR][1000 genomes]
rs34028108	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34092307	0.86[EUR][1000 genomes]
rs34385951	0.86[EUR][1000 genomes]
rs34433746	0.83[EUR][1000 genomes]
rs34452578	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34538548	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34548459	0.83[EUR][1000 genomes]
rs34639984	0.86[EUR][1000 genomes]
rs35371567	0.86[EUR][1000 genomes]
rs35613168	0.86[EUR][1000 genomes]
rs35659175	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35680784	0.84[EUR][1000 genomes]
rs35723696	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35791982	0.86[EUR][1000 genomes]
rs35863408	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771882	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771886	0.81[CHB][hapmap]
rs3771887	0.86[CHB][hapmap]
rs3771888	0.86[CHB][hapmap]
rs3854012	0.83[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664318	0.85[EUR][1000 genomes]
rs4664319	0.88[EUR][1000 genomes]
rs4664320	0.87[EUR][1000 genomes]
rs4664336	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4664347	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4664349	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4665114	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4665137	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4665150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665163	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4665167	0.84[EUR][1000 genomes]
rs4665168	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4665169	0.87[EUR][1000 genomes]
rs4665170	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55775354	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56335263	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56376752	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57201382	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59247111	0.87[EUR][1000 genomes]
rs60956116	0.82[EUR][1000 genomes]
rs6433325	0.86[EUR][1000 genomes]
rs6433327	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs66521733	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66588921	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6705180	0.87[EUR][1000 genomes]
rs6705511	1.00[YRI][hapmap]
rs6708382	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs6713041	0.87[EUR][1000 genomes]
rs6713190	0.85[EUR][1000 genomes]
rs67181317	0.86[EUR][1000 genomes]
rs6723298	0.85[EUR][1000 genomes]
rs67303849	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739517	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6747782	0.86[CHB][hapmap]
rs6751802	0.86[CHB][hapmap]
rs6752471	0.88[EUR][1000 genomes]
rs6752617	0.85[EUR][1000 genomes]
rs6757821	0.82[JPT][hapmap]
rs67693192	0.87[EUR][1000 genomes]
rs67725431	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67868855	0.87[EUR][1000 genomes]
rs71350100	0.84[EUR][1000 genomes]
rs73004003	0.80[EUR][1000 genomes]
rs7558169	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7559296	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7574228	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7587037	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9287955	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs9287956	0.85[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
10	esv1793984	chr2:152138749-152154163	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11683487	TNFAIP6	cis	Whole Blood	GTEx
rs11683487	NMI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152118600-152142800	Weak transcription	Small Intestine	intestine
2	chr2:152118800-152144000	Weak transcription	Stomach Mucosa	stomach
3	chr2:152118800-152144200	Weak transcription	Psoas Muscle	Psoas
4	chr2:152119000-152145000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:152119000-152145200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:152119000-152145200	Weak transcription	NHEK	skin
7	chr2:152119000-152145800	Weak transcription	HSMM	muscle
8	chr2:152119400-152142800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:152119400-152144400	Weak transcription	A549	lung
10	chr2:152119400-152144800	Weak transcription	Brain Substantia Nigra	brain
11	chr2:152119400-152145200	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:152121200-152145000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:152121200-152145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:152125200-152145400	Weak transcription	Aorta	Aorta
15	chr2:152125800-152145200	Weak transcription	Right Ventricle	heart
16	chr2:152126800-152145200	Weak transcription	HMEC	breast
17	chr2:152126800-152145600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:152127000-152145400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:152128000-152144600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:152128400-152145200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:152128600-152145200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:152130200-152145600	Weak transcription	Fetal Kidney	kidney
23	chr2:152130600-152144600	Weak transcription	Fetal Lung	lung
24	chr2:152134400-152144800	Weak transcription	Esophagus	oesophagus
25	chr2:152134400-152145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:152134400-152145400	Weak transcription	Gastric	stomach
27	chr2:152134800-152144800	Weak transcription	Fetal Stomach	stomach
28	chr2:152134800-152144800	Weak transcription	Pancreas	Pancrea
29	chr2:152134800-152144800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:152134800-152145000	Weak transcription	Colonic Mucosa	Colon
31	chr2:152135000-152144600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:152135000-152144800	Weak transcription	Lung	lung
33	chr2:152135000-152145200	Weak transcription	NHLF	lung
34	chr2:152135200-152144800	Weak transcription	Left Ventricle	heart
35	chr2:152135400-152143000	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:152135400-152144800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:152135400-152145200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:152136600-152145200	Weak transcription	NH-A	brain
39	chr2:152136800-152144200	Weak transcription	HUVEC	blood vessel
40	chr2:152137200-152145400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:152137400-152144800	Weak transcription	Osteobl	bone
42	chr2:152137400-152145200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:152137600-152142800	Weak transcription	Spleen	Spleen
44	chr2:152138600-152144200	Weak transcription	Hela-S3	cervix
45	chr2:152139000-152142600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:152139000-152144600	Weak transcription	Brain Anterior Caudate	brain
47	chr2:152139200-152142800	Weak transcription	Primary T cells from cord blood	blood
48	chr2:152139200-152142800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:152139200-152142800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:152139200-152142800	Weak transcription	Ovary	ovary

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