Variant report

Variant	rs2712816
Chromosome Location	chr11:74872576-74872577
allele	A/G
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	POLR2A	chr11:74872430-74872992	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr11:74872513-74872907	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74868174..74871042-chr11:74871954..74874502,2	K562	blood:
2	chr11:74870955..74873792-chr11:74881314..74883069,2	K562	blood:
3	chr11:74868174..74870399-chr11:74871954..74873534,2	K562	blood:
4	chr11:74854253..74855928-chr11:74871794..74874336,2	MCF-7	breast:

Variant related genes	Relation type
SLCO2B1	TF binding region
ENSG00000137491	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10899075	0.88[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1676878	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1944616	0.83[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2018251	0.85[ASN][1000 genomes]
rs2156656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712793	0.83[ASN][1000 genomes]
rs2712795	0.85[ASN][1000 genomes]
rs2712797	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2712799	0.85[ASN][1000 genomes]
rs2712800	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2712801	0.89[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2712802	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712806	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2712808	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712811	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712814	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712815	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712817	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712818	0.89[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap]
rs2851065	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2851067	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2851068	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851069	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2851070	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851071	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851072	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851075	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851079	0.84[JPT][hapmap]
rs2851084	0.84[JPT][hapmap]
rs2851093	0.85[ASN][1000 genomes]
rs2851095	0.85[ASN][1000 genomes]
rs2851097	0.85[ASN][1000 genomes]
rs2851103	0.89[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2851104	0.91[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.90[MKK][hapmap];0.88[ASN][1000 genomes]
rs2851105	0.86[ASN][1000 genomes]
rs2851109	0.91[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851112	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4435030	0.82[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.86[MKK][hapmap]
rs7117575	0.81[MKK][hapmap]
rs870505	0.84[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs870506	0.85[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs875482	0.81[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897919	chr11:74862391-74875501	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2712816	RNF169	cis	cerebellum	SCAN
rs2712816	XRRA1	cis	cerebellum	SCAN
rs2712816	C11orf67	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74863600-74885600	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:74864200-74898400	Weak transcription	Esophagus	oesophagus
3	chr11:74866200-74873000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:74866400-74873000	Weak transcription	Fetal Thymus	thymus
5	chr11:74867400-74873200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:74867600-74875000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:74868600-74875200	Weak transcription	Ovary	ovary
8	chr11:74870000-74872800	Flanking Active TSS	Liver	Liver
9	chr11:74870000-74881000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:74870200-74873400	Enhancers	Adipose Nuclei	Adipose
11	chr11:74870400-74872600	Flanking Active TSS	Fetal Intestine Large	intestine
12	chr11:74870400-74875000	Weak transcription	Small Intestine	intestine
13	chr11:74870800-74901600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:74871200-74872800	Weak transcription	Left Ventricle	heart
15	chr11:74871200-74873000	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:74871200-74873400	Enhancers	HUVEC	blood vessel
17	chr11:74871400-74872800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:74871400-74875200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:74871400-74886800	Weak transcription	Brain Substantia Nigra	brain
20	chr11:74871600-74872600	Weak transcription	Colonic Mucosa	Colon
21	chr11:74871600-74872600	Weak transcription	Fetal Muscle Leg	muscle
22	chr11:74871600-74872800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr11:74871600-74872800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr11:74871600-74872800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr11:74871600-74875000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:74871600-74875600	Enhancers	HepG2	liver
27	chr11:74871800-74872800	Weak transcription	Gastric	stomach
28	chr11:74871800-74872800	Weak transcription	Lung	lung
29	chr11:74871800-74872800	Weak transcription	Pancreas	Pancrea
30	chr11:74871800-74873000	Weak transcription	Spleen	Spleen
31	chr11:74872200-74872600	Weak transcription	Stomach Mucosa	stomach
32	chr11:74872200-74873000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:74872200-74873200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr11:74872200-74873400	Enhancers	Duodenum Mucosa	Duodenum
35	chr11:74872200-74885400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:74872400-74873400	Enhancers	Right Atrium	heart
37	chr11:74872400-74875400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr11:74872400-74876400	Enhancers	Placenta	Placenta
39	chr11:74872400-74883600	Genic enhancers	Fetal Intestine Small	intestine

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