Variant report

Variant	rs28712697
Chromosome Location	chr15:57383219-57383220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57208382..57211323-chr15:57382573..57384078,2	MCF-7	breast:
2	chr15:57382063..57385012-chr15:57386808..57389098,2	K562	blood:
3	chr15:57373645..57376211-chr15:57382766..57385379,2	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10467927	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10467928	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10467929	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11071303	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11071308	0.81[EUR][1000 genomes]
rs11856411	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12101455	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591430	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13379847	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16977222	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16977243	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16977270	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1841697	0.82[EUR][1000 genomes]
rs2169467	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2264904	0.82[AFR][1000 genomes]
rs2593211	0.81[EUR][1000 genomes]
rs2593249	0.81[EUR][1000 genomes]
rs2593250	0.81[EUR][1000 genomes]
rs2593252	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703614	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2733188	0.82[AFR][1000 genomes]
rs2733333	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2733334	0.82[EUR][1000 genomes]
rs28372003	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28422021	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28505122	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28514688	0.81[AFR][1000 genomes]
rs28533433	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28541606	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28648502	0.81[AFR][1000 genomes]
rs28781690	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2927189	0.80[AFR][1000 genomes]
rs2951898	0.86[AFR][1000 genomes]
rs2951899	0.88[AFR][1000 genomes]
rs2957591	0.84[AFR][1000 genomes]
rs58479554	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493900	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67077316	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7163267	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168387	0.81[AFR][1000 genomes]
rs7169053	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7169508	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7171073	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171304	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7176873	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7178833	0.80[AMR][1000 genomes]
rs8023736	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8031640	0.81[AMR][1000 genomes]
rs8032615	0.81[AMR][1000 genomes]
rs8033010	0.83[AMR][1000 genomes]
rs8034502	0.81[EUR][1000 genomes]
rs8035916	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9302200	0.81[EUR][1000 genomes]
rs9806170	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9806199	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28712697	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs28712697	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
5	chr15:57362800-57384200	Weak transcription	HepG2	liver
6	chr15:57365200-57384000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:57365600-57385200	Weak transcription	HSMM	muscle
8	chr15:57365800-57384000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:57372000-57384000	Weak transcription	Dnd41	blood
10	chr15:57372600-57386000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:57372600-57404000	Weak transcription	HSMMtube	muscle
12	chr15:57372600-57404200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:57372800-57384000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:57372800-57384000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr15:57372800-57384400	Weak transcription	Liver	Liver
16	chr15:57372800-57386000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:57372800-57410200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:57373000-57384600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:57373000-57385400	Weak transcription	Primary B cells from cord blood	blood
20	chr15:57373200-57384200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr15:57373200-57384600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:57374000-57385000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr15:57374400-57389400	Weak transcription	NHEK	skin
24	chr15:57374600-57384000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:57374600-57386000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:57374600-57390000	Weak transcription	HMEC	breast
27	chr15:57374600-57398600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr15:57374800-57384400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:57374800-57386800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:57374800-57387800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:57374800-57397800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:57374800-57409600	Weak transcription	Osteobl	bone
33	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
34	chr15:57375000-57385000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:57375000-57386200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:57375000-57386200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:57375000-57393400	Weak transcription	Fetal Intestine Small	intestine
38	chr15:57375000-57398000	Weak transcription	NH-A	brain
39	chr15:57375000-57398400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr15:57376200-57385800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:57376200-57406000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:57376600-57386200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:57376800-57384000	Weak transcription	Fetal Lung	lung
44	chr15:57376800-57397000	Weak transcription	Fetal Stomach	stomach
45	chr15:57378000-57386600	Weak transcription	A549	lung
46	chr15:57378200-57385200	Weak transcription	Fetal Heart	heart
47	chr15:57378200-57385600	Weak transcription	Fetal Intestine Large	intestine
48	chr15:57378200-57386000	Weak transcription	HUVEC	blood vessel
49	chr15:57379400-57386200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:57379400-57390600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links