Variant report

Variant	rs7176873
Chromosome Location	chr15:57349162-57349163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57344217..57346725-chr15:57347528..57349236,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10467927	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs10467928	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10467929	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10851612	0.82[JPT][hapmap]
rs11071303	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071308	0.90[JPT][hapmap];0.89[TSI][hapmap]
rs11853810	0.90[JPT][hapmap]
rs11856210	0.90[JPT][hapmap]
rs11856411	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12101455	0.80[EUR][1000 genomes]
rs12324092	0.82[TSI][hapmap]
rs13379847	0.90[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs1430820	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1430822	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1657922	0.82[JPT][hapmap]
rs16977153	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs16977222	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16977243	0.83[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16977270	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs16977278	0.90[JPT][hapmap];0.89[TSI][hapmap]
rs17415731	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2169467	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2278613	0.82[JPT][hapmap]
rs2414493	0.84[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2439918	0.86[AFR][1000 genomes]
rs2464429	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2464430	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs2470079	0.93[YRI][hapmap]
rs2470082	0.83[ASW][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs2585112	0.81[MKK][hapmap]
rs2593211	0.83[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs2593249	0.90[JPT][hapmap]
rs2593252	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs2615227	0.95[JPT][hapmap]
rs2703576	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs2703580	0.84[MKK][hapmap]
rs2703614	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs2733177	0.86[AFR][1000 genomes]
rs2733188	0.92[YRI][hapmap]
rs2733323	0.81[JPT][hapmap]
rs2733332	0.83[MKK][hapmap]
rs2733333	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs2733334	0.90[JPT][hapmap]
rs28360967	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28372003	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28422021	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28505122	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28533433	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28541606	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28612876	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28648577	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28649108	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28654848	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28677775	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28712697	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28756149	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28814080	0.84[EUR][1000 genomes]
rs28856894	0.81[EUR][1000 genomes]
rs2920265	0.82[AFR][1000 genomes]
rs2920267	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs2951895	0.85[AFR][1000 genomes]
rs2951899	0.83[ASW][hapmap];0.83[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap]
rs2951903	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs2951904	0.83[ASW][hapmap];0.85[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs2951906	0.80[AFR][1000 genomes]
rs2962990	0.82[MKK][hapmap]
rs2962991	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs2962992	0.83[ASW][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs3803453	0.90[JPT][hapmap]
rs4774245	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs58479554	0.80[EUR][1000 genomes]
rs6493900	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6493902	0.92[YRI][hapmap]
rs67077316	0.80[EUR][1000 genomes]
rs7162194	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7163267	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7164655	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7169053	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7171073	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171304	0.88[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173748	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7175191	0.82[JPT][hapmap];0.87[TSI][hapmap]
rs7175436	0.83[ASW][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap]
rs7178833	0.88[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs720290	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs8023343	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs8023736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023816	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8026702	0.90[JPT][hapmap];0.89[TSI][hapmap]
rs8031516	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8031640	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8032615	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033010	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8034066	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8034502	0.90[JPT][hapmap]
rs8034744	0.83[TSI][hapmap]
rs8035485	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs8035916	0.83[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs8039899	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8040708	0.87[EUR][1000 genomes]
rs9302200	0.92[CEU][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9672676	0.83[TSI][hapmap]
rs9806170	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9806199	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs997683	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7176873	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs7176873	AQP9	cis	cerebellum	SCAN
rs7176873	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324400-57349200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
3	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:57324800-57349400	Weak transcription	Right Ventricle	heart
5	chr15:57328200-57353600	Weak transcription	Pancreas	Pancrea
6	chr15:57328600-57355000	Weak transcription	Dnd41	blood
7	chr15:57329800-57349600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:57329800-57351400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:57332000-57349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:57332000-57349400	Weak transcription	Thymus	Thymus
11	chr15:57332000-57355800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr15:57333400-57349400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:57336600-57349200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:57336600-57371800	Weak transcription	K562	blood
15	chr15:57337400-57349200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:57337600-57351200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:57338200-57350000	Weak transcription	Fetal Heart	heart
18	chr15:57339200-57350000	Weak transcription	HSMM	muscle
19	chr15:57339600-57349800	Weak transcription	Primary T cells from cord blood	blood
20	chr15:57339600-57349800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:57339600-57355600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:57339800-57361600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr15:57341800-57349400	Weak transcription	NH-A	brain
25	chr15:57341800-57349800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:57343800-57363400	Weak transcription	Aorta	Aorta
27	chr15:57344000-57349200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:57344000-57349200	Weak transcription	GM12878-XiMat	blood
29	chr15:57344000-57349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:57344000-57351400	Weak transcription	Fetal Brain Female	brain
31	chr15:57344400-57351400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:57344600-57363600	Weak transcription	Right Atrium	heart
33	chr15:57345200-57349200	Weak transcription	NHDF-Ad	bronchial
34	chr15:57345600-57349400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:57346000-57349200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:57346200-57349400	Weak transcription	Small Intestine	intestine
38	chr15:57346400-57352800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:57346600-57349200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:57346600-57349200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:57346600-57349600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:57346600-57355000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr15:57346800-57349200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:57346800-57349200	Weak transcription	A549	lung
45	chr15:57346800-57349600	Weak transcription	Liver	Liver
46	chr15:57346800-57351400	Weak transcription	HSMMtube	muscle
47	chr15:57347000-57349200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:57347000-57349200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr15:57347000-57349200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:57347000-57349200	Weak transcription	Muscle Satellite Cultured Cells	--

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