Variant report

Variant	rs7171304
Chromosome Location	chr15:57341366-57341367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10467927	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs10467928	0.89[CEU][hapmap]
rs10467929	0.89[CEU][hapmap]
rs11071303	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856411	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12101455	0.80[EUR][1000 genomes]
rs13379847	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs1430820	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1430822	1.00[CEU][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16977153	0.90[CEU][hapmap]
rs16977222	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16977243	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16977270	0.90[CEU][hapmap]
rs17415731	0.90[CEU][hapmap];0.80[ASN][1000 genomes]
rs2169467	1.00[CEU][hapmap]
rs2414493	0.88[CEU][hapmap]
rs2435907	0.80[AFR][1000 genomes]
rs2439918	0.82[AFR][1000 genomes]
rs2464429	0.86[YRI][hapmap]
rs2464430	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs2470079	0.83[YRI][hapmap]
rs2470082	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs2593252	0.90[CEU][hapmap]
rs2703576	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs2703614	1.00[CEU][hapmap]
rs2733177	0.82[AFR][1000 genomes]
rs2733188	0.91[YRI][hapmap]
rs2733333	1.00[CEU][hapmap]
rs28360967	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28372003	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28422021	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28505122	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28533433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28541606	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28612876	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28648577	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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];0.83[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]
rs28756149	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28814080	0.84[EUR][1000 genomes]
rs28856894	0.81[EUR][1000 genomes]
rs2920265	0.84[AFR][1000 genomes]
rs2920267	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs2951895	0.83[AFR][1000 genomes]
rs2951899	0.90[YRI][hapmap]
rs2951903	0.91[YRI][hapmap]
rs2951904	0.90[YRI][hapmap]
rs2951906	0.82[AFR][1000 genomes]
rs2957574	0.84[AFR][1000 genomes]
rs2962991	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs2962992	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs4774245	0.90[CEU][hapmap]
rs58479554	0.80[EUR][1000 genomes]
rs6493900	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493902	0.90[YRI][hapmap]
rs67077316	0.80[EUR][1000 genomes]
rs7162194	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7163267	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7164655	1.00[CEU][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7169053	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7171073	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175436	0.81[YRI][hapmap]
rs7176873	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]
rs7178833	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8023343	0.90[CEU][hapmap]
rs8023736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8023816	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8031516	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8031640	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8032615	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8033010	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8034066	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8035485	0.88[CEU][hapmap]
rs8035916	0.90[CEU][hapmap]
rs8039899	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8040708	0.87[EUR][1000 genomes]
rs9302200	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9806170	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9806199	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7171304	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs7171304	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57311000-57347000	Weak transcription	Fetal Intestine Large	intestine
2	chr15:57316400-57345400	Weak transcription	Fetal Intestine Small	intestine
3	chr15:57324400-57349200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
5	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
6	chr15:57324800-57347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:57324800-57349400	Weak transcription	Right Ventricle	heart
8	chr15:57328200-57353600	Weak transcription	Pancreas	Pancrea
9	chr15:57328400-57343800	Weak transcription	Small Intestine	intestine
10	chr15:57328400-57345800	Weak transcription	Left Ventricle	heart
11	chr15:57328600-57355000	Weak transcription	Dnd41	blood
12	chr15:57329800-57349600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:57329800-57351400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:57330400-57343400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:57332000-57345200	Weak transcription	HepG2	liver
16	chr15:57332000-57346000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:57332000-57349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:57332000-57349400	Weak transcription	Thymus	Thymus
19	chr15:57332000-57355800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr15:57332800-57343800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:57332800-57345800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:57333400-57349400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:57334000-57345000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:57334000-57346000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:57334000-57346200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:57334200-57343600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:57335000-57347400	Weak transcription	Lung	lung
28	chr15:57335200-57341400	Weak transcription	Fetal Kidney	kidney
29	chr15:57335200-57341600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:57335400-57349000	Weak transcription	NHEK	skin
31	chr15:57335600-57345400	Weak transcription	HUVEC	blood vessel
32	chr15:57335800-57343400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:57336400-57341400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:57336400-57345000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr15:57336600-57349200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:57336600-57371800	Weak transcription	K562	blood
37	chr15:57336800-57346000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:57336800-57349000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:57337000-57341800	Strong transcription	Fetal Thymus	thymus
40	chr15:57337200-57345800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:57337400-57342000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:57337400-57349200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:57337600-57345600	Weak transcription	Fetal Lung	lung
44	chr15:57337600-57351200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:57338200-57341400	Weak transcription	Brain Angular Gyrus	brain
46	chr15:57338200-57341600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr15:57338200-57343800	Weak transcription	Right Atrium	heart
48	chr15:57338200-57350000	Weak transcription	Fetal Heart	heart
49	chr15:57338600-57341400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:57338600-57345000	Weak transcription	Colon Smooth Muscle	Colon

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