Variant report

Variant	rs8032615
Chromosome Location	chr15:57300851-57300852
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57208974..57212376-chr15:57299847..57301988,3	MCF-7	breast:
2	chr15:57300673..57301307-chr5:172483325..172483972,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164463	Chromatin interaction
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10467927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10467928	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs10467929	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs10851612	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs11071303	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11071308	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1115019	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11856210	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs11856411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12901355	0.84[EUR][1000 genomes]
rs13379847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1430820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1430822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1441236	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1657922	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs16977153	0.87[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs16977222	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16977243	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs16977270	0.87[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs16977278	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs17415731	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1820994	0.81[ASN][1000 genomes]
rs2169467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs2278613	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2593211	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2593249	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2593252	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2703614	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2733333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2733334	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs28360967	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28372003	0.83[AMR][1000 genomes]
rs28422021	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28505122	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28533433	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28541606	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28612876	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28616268	0.85[EUR][1000 genomes]
rs28648577	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28649108	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28654848	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28677775	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28712697	0.81[AMR][1000 genomes]
rs28756149	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28814080	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28856894	0.88[EUR][1000 genomes]
rs4774245	0.87[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs6493900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes]
rs7162194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7163267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes]
rs7164655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7169053	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7171304	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7173748	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7175191	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7176873	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]
rs7178833	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8023343	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs8023736	0.87[AMR][1000 genomes]
rs8023816	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8026702	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs8031516	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8031640	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033010	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034502	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs8035485	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs8035916	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs8039899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040708	0.94[EUR][1000 genomes]
rs9302200	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9806170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs9806199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
rs8032615	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs8032615	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57273000-57307200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:57275400-57306200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:57279600-57301800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:57282000-57307400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:57282000-57315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr15:57282200-57308400	Weak transcription	Thymus	Thymus
10	chr15:57282200-57311000	Weak transcription	K562	blood
11	chr15:57282200-57315200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr15:57282600-57306200	Weak transcription	HepG2	liver
13	chr15:57284200-57310800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:57286000-57306200	Weak transcription	Fetal Intestine Large	intestine
15	chr15:57286000-57307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:57286200-57307600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:57286200-57307600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:57286200-57312000	Weak transcription	HSMM	muscle
19	chr15:57286200-57314800	Weak transcription	Dnd41	blood
20	chr15:57286400-57309400	Weak transcription	Fetal Lung	lung
21	chr15:57288800-57307400	Weak transcription	HMEC	breast
22	chr15:57289400-57304600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:57289400-57308000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:57289600-57315200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:57289600-57315600	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:57289800-57315600	Weak transcription	Primary B cells from cord blood	blood
27	chr15:57294200-57307400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:57294400-57311600	Weak transcription	GM12878-XiMat	blood
29	chr15:57295200-57313600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:57296000-57301400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:57296000-57307600	Weak transcription	Brain Substantia Nigra	brain
32	chr15:57296000-57308800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:57296000-57308800	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:57296200-57301600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:57296200-57302800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:57296200-57303800	Weak transcription	HUVEC	blood vessel
37	chr15:57296200-57304600	Weak transcription	Brain Anterior Caudate	brain
38	chr15:57296200-57307400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:57296200-57307600	Weak transcription	A549	lung
40	chr15:57296200-57308000	Weak transcription	NH-A	brain
41	chr15:57296400-57309400	Weak transcription	NHDF-Ad	bronchial
42	chr15:57296400-57310200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:57296600-57313200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:57297200-57308000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:57297200-57316800	Weak transcription	Fetal Stomach	stomach
46	chr15:57297800-57307200	Weak transcription	Pancreas	Pancrea
47	chr15:57298200-57307600	Weak transcription	Gastric	stomach
48	chr15:57299000-57307600	Weak transcription	Ovary	ovary
49	chr15:57299200-57316000	Weak transcription	Right Ventricle	heart
50	chr15:57299200-57317200	Weak transcription	Esophagus	oesophagus

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