Variant report

Variant	rs1875124
Chromosome Location	chr12:58196802-58196803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr12:58196693-58197767	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr12:58196779-58197728	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr12:58196800-58196950	GM12870	blood:	n/a	n/a
4	CTCF	chr12:58196418-58197741	A549	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58196798..58197728-chr12:58208612..58210054,6	MCF-7	breast:
2	chr12:58195714..58198546-chr12:58205658..58208467,2	K562	blood:
3	chr12:58193274..58197647-chr12:58200040..58205215,7	MCF-7	breast:
4	chr12:57912401..57915240-chr12:58195290..58197109,2	MCF-7	breast:
5	chr12:58193083..58195833-chr12:58196362..58200712,4	K562	blood:
6	chr12:58194136..58195833-chr12:58195975..58197862,2	K562	blood:
7	chr12:58148177..58150864-chr12:58195789..58197895,2	MCF-7	breast:
8	chr12:58196723..58199553-chr12:58199752..58203414,5	K562	blood:

No data

Variant related genes	Relation type
AVIL	TF binding region
ENSG00000270039	TF binding region
ENSG00000269903	Chromatin interaction
ENSG00000206749	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000139266	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1021469	0.92[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10431505	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10431552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747786	0.83[JPT][hapmap]
rs10747787	0.83[JPT][hapmap]
rs10783847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783850	1.00[LWK][hapmap]
rs10783851	1.00[LWK][hapmap]
rs10783853	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10877011	0.85[CEU][hapmap];0.80[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10877012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877013	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877017	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877018	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877029	0.83[JPT][hapmap]
rs10877030	0.83[JPT][hapmap]
rs11172333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172342	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172350	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172351	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172367	0.83[JPT][hapmap]
rs11172369	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs11172371	1.00[YRI][hapmap]
rs1599931	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs1599932	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1689585	0.83[GIH][hapmap]
rs1875125	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs2014886	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2069502	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2069506	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291617	1.00[CEU][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782130	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3825079	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4237844	0.83[JPT][hapmap];0.85[YRI][hapmap]
rs4646536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760171	0.83[JPT][hapmap]
rs4760172	0.83[JPT][hapmap]
rs4760332	0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs4760339	0.82[JPT][hapmap]
rs4760341	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs56177740	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs701008	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs703842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs724834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312623	0.83[JPT][hapmap]
rs7965287	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8181644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs870392	0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs871871	0.88[JPT][hapmap]
rs923829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9652011	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs1875124	TSFM	cis	parietal	SCAN
rs1875124	FAM119B	cis	lymphoblastoid	seeQTL
rs1875124	METTL21B	cis	Esophagus Muscularis	GTEx
rs1875124	TSFM	cis	lymphoblastoid	seeQTL
rs1875124	FAM119B	cis	cerebellum	SCAN
rs1875124	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1875124	GPR84	cis	cerebellum	SCAN
rs1875124	KRT5	cis	cerebellum	SCAN
rs1875124	TSFM	cis	cerebellum	SCAN
rs1875124	TSPAN31	cis	cerebellum	SCAN
rs1875124	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs1875124	TSFM	cis	Muscle Skeletal	GTEx
rs1875124	CDK4	cis	cerebellum	SCAN
rs1875124	RP11-571M6.13	cis	Thyroid	GTEx
rs1875124	METTL21B	cis	Muscle Skeletal	GTEx
rs1875124	METTL21B	cis	Heart Left Ventricle	GTEx
rs1875124	WIBG	cis	cerebellum	SCAN
rs1875124	CYP27B1	cis	Thyroid	GTEx
rs1875124	KIAA0748	cis	cerebellum	SCAN
rs1875124	METTL21B	cis	Adipose Subcutaneous	GTEx
rs1875124	METTL21B	cis	Esophagus Mucosa	GTEx
rs1875124	METTL21B	cis	Whole Blood	GTEx
rs1875124	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs1875124	ESPL1	cis	parietal	SCAN
rs1875124	TSPAN31	cis	parietal	SCAN
rs1875124	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs1875124	METTL21B	cis	lung	GTEx
rs1875124	FAM119B	cis	parietal	SCAN
rs1875124	HSD17B6	cis	cerebellum	SCAN
rs1875124	TSFM	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58177200-58197200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:58177400-58200400	Weak transcription	Fetal Heart	heart
3	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:58177800-58198400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr12:58177800-58198400	Strong transcription	Fetal Muscle Leg	muscle
6	chr12:58177800-58199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:58178000-58197200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr12:58178000-58197600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:58178000-58198200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:58178000-58198200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:58178000-58198200	Strong transcription	Fetal Thymus	thymus
12	chr12:58178200-58197000	Strong transcription	Fetal Intestine Large	intestine
13	chr12:58178200-58197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:58178200-58198200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:58178600-58207600	Strong transcription	Liver	Liver
16	chr12:58179000-58197600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:58179000-58198200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:58179200-58199000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:58179400-58197400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr12:58181400-58216000	Weak transcription	Fetal Brain Male	brain
21	chr12:58183000-58198200	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr12:58185400-58197000	Strong transcription	Fetal Brain Female	brain
23	chr12:58185600-58198800	Strong transcription	Primary T cells from cord blood	blood
24	chr12:58185800-58197000	Strong transcription	Brain Germinal Matrix	brain
25	chr12:58186600-58198200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:58187000-58216600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:58187200-58215600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:58187400-58197200	Strong transcription	Brain Anterior Caudate	brain
29	chr12:58188400-58197200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:58188600-58207800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:58189000-58197200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr12:58189000-58208400	Strong transcription	Fetal Stomach	stomach
33	chr12:58189200-58207800	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:58189400-58197200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:58189400-58197200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:58189400-58197200	Strong transcription	Osteobl	bone
37	chr12:58189400-58197400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:58189400-58198200	Strong transcription	NHLF	lung
39	chr12:58189400-58207200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:58189600-58197200	Strong transcription	Colon Smooth Muscle	Colon
41	chr12:58189600-58197400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:58189600-58197600	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:58189600-58200200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:58189800-58197000	Strong transcription	Left Ventricle	heart
45	chr12:58189800-58197200	Strong transcription	HSMMtube	muscle
46	chr12:58189800-58198400	Strong transcription	NHDF-Ad	bronchial
47	chr12:58189800-58208400	Strong transcription	Placenta	Placenta
48	chr12:58190200-58216600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:58190400-58197400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:58190400-58201000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links