Variant report

Variant	rs2712800
Chromosome Location	chr11:74852100-74852101
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr11:74851491-74852590	IMR90	lung:	n/a	chr11:74852333-74852344 chr11:74852332-74852347
2	CTCF	chr11:74851244-74852225	HCT-116	colon:	n/a	n/a
3	RAD21	chr11:74851456-74852187	MCF-7	breast:	n/a	chr11:74851557-74851566
4	RAD21	chr11:74851540-74852118	A549	lung:	n/a	chr11:74851557-74851566
5	CTCF	chr11:74852080-74852230	GM12873	blood:	n/a	n/a
6	RAD21	chr11:74851461-74852103	ECC-1	luminal epithelium:	n/a	chr11:74851557-74851566
7	CTCF	chr11:74851501-74852116	MCF-7	breast:	n/a	n/a
8	RAD21	chr11:74851482-74852101	ECC-1	luminal epithelium:	n/a	chr11:74851557-74851566
9	CTCF	chr11:74851526-74852221	HCT-116	colon:	n/a	n/a
10	CTCF	chr11:74851269-74852307	SK-N-SH	brain:	n/a	n/a
11	CTCF	chr11:74851113-74852476	A549	lung:	n/a	n/a
12	SMC3	chr11:74850980-74852584	SK-N-SH	brain:	n/a	chr11:74851758-74851765
13	RAD21	chr11:74851238-74852373	SK-N-SH	brain:	n/a	chr11:74851557-74851566
14	WRNIP1	chr11:74851729-74852104	GM12878	blood:	n/a	n/a
15	RAD21	chr11:74851478-74852224	HCT-116	colon:	n/a	chr11:74851557-74851566
16	CTCF	chr11:74852020-74852170	GM12871	blood:	n/a	n/a
17	CTCF	chr11:74852060-74852210	HEK293	kidney:	n/a	n/a
18	CTCF	chr11:74851487-74852171	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74851287..74852438-chr11:74958974..74960362,6	MCF-7	breast:
2	chr11:74851263..74852476-chr11:74952166..74953375,10	MCF-7	breast:
3	chr11:74733882..74734577-chr11:74851528..74852418,2	MCF-7	breast:
4	chr11:74851665..74854336-chr11:74855499..74858438,2	MCF-7	breast:
5	chr11:74851266..74852245-chr11:74959366..74960342,8	K562	blood:
6	chr11:74849283..74850784-chr11:74852080..74854069,2	K562	blood:
7	chr11:74851279..74852245-chr11:74915585..74916634,10	MCF-7	breast:
8	chr11:74851375..74852262-chr11:74959346..74960408,13	MCF-7	breast:
9	chr11:74640882..74641396-chr11:74851634..74852513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255395	TF binding region
ENSG00000255136	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10899075	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1944615	0.87[ASN][1000 genomes]
rs1944616	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018251	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2156656	0.88[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2465290	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2712786	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2712788	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap]
rs2712793	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712794	0.83[ASN][1000 genomes]
rs2712795	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2712797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712799	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712801	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2712802	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2712806	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712808	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712809	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712811	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712815	0.83[ASN][1000 genomes]
rs2712816	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2712817	0.85[ASN][1000 genomes]
rs2712818	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2851065	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851067	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851068	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2851069	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851070	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2851071	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2851072	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2851075	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2851078	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap]
rs2851079	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2851080	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2851081	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2851082	0.85[JPT][hapmap]
rs2851084	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs2851086	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2851093	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851095	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851097	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851103	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851104	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851105	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851107	0.84[ASN][1000 genomes]
rs2851109	0.88[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs2851112	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4335576	0.85[JPT][hapmap]
rs4435030	0.92[CEU][hapmap];0.94[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs4944067	0.85[JPT][hapmap]
rs7121374	0.85[JPT][hapmap]
rs870505	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs870506	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875482	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

mRNA abundance (count:33)

SNP	Gene	Cis/trans	Tissue	Source
rs2712800	OR4D6	cis	Liver	GTEx
rs2712800	THRSP	cis	parietal	SCAN
rs2712800	ACVRL1	trans	multi-tissue	Pritchard
rs2712800	NTRK3	cis	Liver	GTEx
rs2712800	CACNA1S	trans	multi-tissue	Pritchard
rs2712800	hCT1844212.1	trans	multi-tissue	Pritchard
rs2712800	GPR27	cis	Liver	GTEx
rs2712800	HSS00128295	trans	multi-tissue	Pritchard
rs2712800	CACNA1C	cis	Liver	GTEx
rs2712800	SLCO2B1	cis	multi-tissue	Pritchard
rs2712800	BC039366	cis	multi-tissue	Pritchard
rs2712800	GPR27	trans	multi-tissue	Pritchard
rs2712800	CCDC57	cis	Liver	GTEx
rs2712800	INPPL1	cis	parietal	SCAN
rs2712800	CRYGD	trans	parietal	SCAN
rs2712800	FBXO42	trans	parietal	SCAN
rs2712800	XM_211129	trans	multi-tissue	Pritchard
rs2712800	hCT1642432	trans	multi-tissue	Pritchard
rs2712800	RNF169	cis	cerebellum	SCAN
rs2712800	ITGA3	cis	Liver	GTEx
rs2712800	ITGA3	trans	multi-tissue	Pritchard
rs2712800	FCHSD2	cis	cerebellum	SCAN
rs2712800	KLHL35	cis	Liver	GTEx
rs2712800	CACNA1S	cis	Liver	GTEx
rs2712800	BC037286	trans	multi-tissue	Pritchard
rs2712800	XRRA1	cis	cerebellum	SCAN
rs2712800	HSS00085450	trans	multi-tissue	Pritchard
rs2712800	XM_087553	trans	multi-tissue	Pritchard
rs2712800	CCDC57	trans	multi-tissue	Pritchard
rs2712800	NTRK3	trans	multi-tissue	Pritchard
rs2712800	NM_173583	cis	multi-tissue	Pritchard
rs2712800	ACVRL1	cis	Liver	GTEx
rs2712800	OR4D6	trans	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74846600-74853800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:74847000-74853800	Weak transcription	Adipose Nuclei	Adipose
3	chr11:74847200-74852400	Weak transcription	K562	blood
4	chr11:74851200-74852400	Enhancers	GM12878-XiMat	blood
5	chr11:74851400-74852200	Enhancers	Primary B cells from peripheral blood	blood
6	chr11:74851400-74852200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:74851400-74852200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:74851400-74852200	Enhancers	Fetal Intestine Small	intestine
9	chr11:74851400-74852400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:74851400-74855600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr11:74851600-74852400	Enhancers	Pancreas	Pancrea
12	chr11:74851600-74852400	Enhancers	Stomach Mucosa	stomach
13	chr11:74851600-74852600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr11:74851600-74855800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr11:74851800-74852200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:74851800-74852200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:74851800-74852400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr11:74851800-74852400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:74851800-74852400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr11:74851800-74852400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr11:74851800-74852400	Enhancers	HepG2	liver
22	chr11:74851800-74852600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr11:74851800-74852600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr11:74851800-74852600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr11:74851800-74853600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr11:74851800-74854400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr11:74852000-74852200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
28	chr11:74852000-74853600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:74852000-74853800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:74852000-74853800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:74852000-74853800	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:74852000-74853800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr11:74852000-74853800	Weak transcription	Fetal Thymus	thymus
34	chr11:74852000-74854000	Weak transcription	Fetal Intestine Large	intestine
35	chr11:74852000-74854000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:74852000-74854400	Weak transcription	Liver	Liver
37	chr11:74852000-74861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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