Variant report

Variant	rs7164655
Chromosome Location	chr15:57238149-57238150
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57222920..57225645-chr15:57236445..57240161,3	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10467927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap]
rs10851612	0.87[CHB][hapmap]
rs11071303	0.83[EUR][1000 genomes]
rs1115019	0.83[CHB][hapmap]
rs11856411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12324092	0.82[EUR][1000 genomes]
rs12901355	0.84[EUR][1000 genomes]
rs13379847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap]
rs1430820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1430822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1441236	0.83[CHB][hapmap]
rs1657922	0.83[CHB][hapmap]
rs16977153	0.87[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs16977222	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16977243	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs17415731	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2169467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2278613	0.87[CHB][hapmap]
rs2464429	0.86[YRI][hapmap]
rs2464430	0.87[YRI][hapmap]
rs2470079	0.84[YRI][hapmap]
rs2470082	0.86[YRI][hapmap]
rs2703576	0.90[YRI][hapmap]
rs2733188	0.90[YRI][hapmap]
rs2733333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs28360967	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28422021	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28505122	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28533433	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28541606	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28612876	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28616268	0.85[EUR][1000 genomes]
rs28648577	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28649108	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28654848	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28677775	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28756149	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28814080	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28856894	0.95[EUR][1000 genomes]
rs2920267	0.89[YRI][hapmap]
rs2951899	0.88[YRI][hapmap]
rs2951903	0.90[YRI][hapmap]
rs2951904	0.89[YRI][hapmap]
rs2962991	0.86[YRI][hapmap]
rs2962992	0.82[YRI][hapmap]
rs4774245	0.87[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6493900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs67149912	0.84[EUR][1000 genomes]
rs7162194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7163267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap]
rs7169053	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7171073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7171304	1.00[CEU][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7175191	0.87[CHB][hapmap]
rs7175436	0.82[YRI][hapmap]
rs7176873	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]
rs7178030	0.80[EUR][1000 genomes]
rs7178833	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs8023343	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs8023816	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8031516	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8031640	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8032615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8033010	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8034066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8035485	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs8035916	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs8039899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8040708	0.94[EUR][1000 genomes]
rs9302200	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs9806170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap]
rs9806199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7164655	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs7164655	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
2	chr15:57212600-57241000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:57216400-57241800	Weak transcription	Fetal Brain Male	brain
5	chr15:57222600-57250200	Weak transcription	NH-A	brain
6	chr15:57222800-57240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:57222800-57255000	Weak transcription	HMEC	breast
8	chr15:57223200-57240400	Weak transcription	Aorta	Aorta
9	chr15:57224600-57248600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:57225000-57239400	Weak transcription	Left Ventricle	heart
11	chr15:57225000-57244200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:57225000-57249000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:57226400-57242000	Weak transcription	HUVEC	blood vessel
14	chr15:57227000-57249800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:57227600-57260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:57228000-57242400	Weak transcription	Fetal Intestine Small	intestine
17	chr15:57228200-57260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:57229400-57255800	Weak transcription	Fetal Stomach	stomach
19	chr15:57231200-57240800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:57232000-57256000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:57232200-57238200	Weak transcription	Small Intestine	intestine
22	chr15:57232200-57240000	Weak transcription	NHLF	lung
23	chr15:57232600-57239200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:57233000-57250200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:57233200-57238800	Weak transcription	HepG2	liver
26	chr15:57233800-57239400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:57233800-57242000	Weak transcription	Ovary	ovary
28	chr15:57234200-57240800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:57234400-57239200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr15:57234400-57249000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:57235200-57239400	Weak transcription	Thymus	Thymus
32	chr15:57236000-57239800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:57236200-57238200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:57236200-57239200	Strong transcription	Fetal Thymus	thymus
35	chr15:57236200-57239800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:57236200-57240400	Weak transcription	Osteobl	bone
37	chr15:57236400-57238400	Strong transcription	Dnd41	blood
38	chr15:57236600-57238400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:57236800-57238600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr15:57236800-57238600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
41	chr15:57236800-57249800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:57237000-57239400	Weak transcription	Brain Angular Gyrus	brain
43	chr15:57237000-57242000	Weak transcription	Brain Anterior Caudate	brain
44	chr15:57237200-57238400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:57237200-57238600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:57237200-57240400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:57237200-57241800	Weak transcription	Fetal Heart	heart
48	chr15:57237400-57238200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
49	chr15:57237400-57238200	Strong transcription	HSMM	muscle
50	chr15:57237400-57238800	ZNF genes & repeats	Primary B cells from cord blood	blood

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