Variant report

Variant	rs13004590
Chromosome Location	chr2:152127699-152127700
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152119643..152123039-chr2:152125145..152128347,3	MCF-7	breast:
2	chr2:152116138..152121069-chr2:152127385..152131823,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184898	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10165186	0.84[EUR][1000 genomes]
rs10165284	0.84[EUR][1000 genomes]
rs10169816	0.83[JPT][hapmap]
rs10184314	0.85[EUR][1000 genomes]
rs10201139	0.84[EUR][1000 genomes]
rs10203366	0.85[EUR][1000 genomes]
rs10207408	0.84[EUR][1000 genomes]
rs10209942	0.84[EUR][1000 genomes]
rs10210155	0.84[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];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11678123	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11678951	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11680338	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11683487	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]
rs11691055	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11691217	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs12467046	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12469634	1.00[YRI][hapmap]
rs12471191	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12476687	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12624156	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12693004	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12987765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs12996459	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12998170	0.85[EUR][1000 genomes]
rs13001328	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13007728	0.86[EUR][1000 genomes]
rs13015862	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13020769	0.85[EUR][1000 genomes]
rs13020962	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13025888	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13027425	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13030194	0.84[EUR][1000 genomes]
rs13412131	0.84[EUR][1000 genomes]
rs13420739	0.85[EUR][1000 genomes]
rs17796622	1.00[YRI][hapmap]
rs17798290	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113508	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2194492	0.85[EUR][1000 genomes]
rs2218880	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271811	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278090	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28416443	0.82[EUR][1000 genomes]
rs2880488	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs289829	0.86[CHB][hapmap]
rs289906	0.82[EUR][1000 genomes]
rs289923	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs289924	0.84[AMR][1000 genomes]
rs34028108	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34092307	0.84[EUR][1000 genomes]
rs34385951	0.84[EUR][1000 genomes]
rs34433746	0.81[EUR][1000 genomes]
rs34452578	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34538548	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34548459	0.81[EUR][1000 genomes]
rs34639984	0.84[EUR][1000 genomes]
rs35371567	0.84[EUR][1000 genomes]
rs35613168	0.84[EUR][1000 genomes]
rs35659175	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35680784	0.82[EUR][1000 genomes]
rs35723696	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35791982	0.84[EUR][1000 genomes]
rs35863408	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3771882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771886	0.81[CHB][hapmap]
rs3771887	0.86[CHB][hapmap]
rs3771888	0.86[CHB][hapmap]
rs3854012	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664318	0.83[EUR][1000 genomes]
rs4664319	0.86[EUR][1000 genomes]
rs4664320	0.85[EUR][1000 genomes]
rs4664336	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4664347	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4664349	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4665114	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4665137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4665163	0.85[EUR][1000 genomes]
rs4665167	0.82[EUR][1000 genomes]
rs4665168	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4665169	0.85[EUR][1000 genomes]
rs4665170	0.82[EUR][1000 genomes]
rs55775354	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56335263	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56376752	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57201382	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59247111	0.85[EUR][1000 genomes]
rs60956116	0.81[EUR][1000 genomes]
rs6433325	0.84[EUR][1000 genomes]
rs6433327	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs66521733	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66588921	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6705180	0.85[EUR][1000 genomes]
rs6705511	1.00[YRI][hapmap]
rs6708382	0.85[EUR][1000 genomes]
rs6713041	0.85[EUR][1000 genomes]
rs6713190	0.83[EUR][1000 genomes]
rs67181317	0.84[EUR][1000 genomes]
rs6723298	0.83[EUR][1000 genomes]
rs67303849	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6739517	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6747782	0.86[CHB][hapmap]
rs6751802	0.86[CHB][hapmap]
rs6752471	0.86[EUR][1000 genomes]
rs6752617	0.83[EUR][1000 genomes]
rs6757821	0.82[JPT][hapmap]
rs67693192	0.85[EUR][1000 genomes]
rs67725431	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67868855	0.85[EUR][1000 genomes]
rs71350100	0.82[EUR][1000 genomes]
rs7558169	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7559296	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7574228	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7587037	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9287955	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs9287956	0.83[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13004590	TNFAIP6	cis	Whole Blood	GTEx
rs13004590	NMI	Cis_1M	lymphoblastoid	RTeQTL
rs13004590	RBM43	cis	Whole Blood	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152118600-152133800	Weak transcription	Gastric	stomach
2	chr2:152118600-152142800	Weak transcription	Small Intestine	intestine
3	chr2:152118800-152129800	Weak transcription	Colonic Mucosa	Colon
4	chr2:152118800-152130000	Weak transcription	Fetal Stomach	stomach
5	chr2:152118800-152130600	Weak transcription	Fetal Intestine Small	intestine
6	chr2:152118800-152133800	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:152118800-152134000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:152118800-152144000	Weak transcription	Stomach Mucosa	stomach
9	chr2:152118800-152144200	Weak transcription	Psoas Muscle	Psoas
10	chr2:152119000-152129400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:152119000-152132000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:152119000-152133600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:152119000-152134200	Weak transcription	NHLF	lung
14	chr2:152119000-152137000	Weak transcription	Osteobl	bone
15	chr2:152119000-152145000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:152119000-152145200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:152119000-152145200	Weak transcription	NHEK	skin
18	chr2:152119000-152145800	Weak transcription	HSMM	muscle
19	chr2:152119200-152128800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:152119200-152133200	Weak transcription	NHDF-Ad	bronchial
21	chr2:152119200-152133800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:152119400-152128800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:152119400-152138200	Weak transcription	Hela-S3	cervix
24	chr2:152119400-152142800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:152119400-152144400	Weak transcription	A549	lung
26	chr2:152119400-152144800	Weak transcription	Brain Substantia Nigra	brain
27	chr2:152119400-152145200	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:152119600-152132000	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:152119600-152133400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:152121200-152130200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:152121200-152133000	Weak transcription	HSMMtube	muscle
32	chr2:152121200-152133800	Weak transcription	Pancreas	Pancrea
33	chr2:152121200-152138000	Weak transcription	K562	blood
34	chr2:152121200-152145000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:152121200-152145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:152121400-152128600	Weak transcription	Fetal Lung	lung
37	chr2:152124400-152138400	Weak transcription	Brain Anterior Caudate	brain
38	chr2:152124600-152139200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:152125200-152145400	Weak transcription	Aorta	Aorta
40	chr2:152125800-152139200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:152125800-152145200	Weak transcription	Right Ventricle	heart
42	chr2:152126000-152139200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:152126200-152129400	Strong transcription	GM12878-XiMat	blood
44	chr2:152126200-152139200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:152126200-152139200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:152126200-152139200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:152126200-152139400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:152126200-152139400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:152126200-152139400	Strong transcription	Placenta	Placenta
50	chr2:152126200-152139800	Strong transcription	Monocytes-CD14+_RO01746	blood

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