Variant report

Variant	rs12901812
Chromosome Location	chr15:78365218-78365219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:78365080-78365230	HMF	breast:	n/a	n/a
2	CTCF	chr15:78365100-78365250	AG04450	lung:	n/a	n/a
3	POLR2A	chr15:78364590-78365313	SK-N-MC	brain:	n/a	n/a
4	STAT1	chr15:78364834-78365426	Hela-S3	cervix:	n/a	chr15:78365137-78365148 chr15:78365007-78365015
5	CTCF	chr15:78365160-78365310	AG09319	gingival:	n/a	n/a
6	USF1	chr15:78364965-78365246	SK-N-SH	brain:	n/a	chr15:78365104-78365115
7	CTCF	chr15:78365100-78365250	BJ	skin:	n/a	n/a
8	CTCF	chr15:78365100-78365250	AG09309	skin:	n/a	n/a
9	CTCF	chr15:78365160-78365310	BJ	skin:	n/a	n/a
10	CTCF	chr15:78365080-78365230	AG10803	skin:	n/a	n/a
11	CTCF	chr15:78365120-78365270	HPAF	blood vessel:	n/a	n/a
12	CTCF	chr15:78365100-78365250	NHDF-neo	bronchial:	n/a	n/a
13	CTCF	chr15:78365180-78365330	AG04449	skin:	n/a	n/a
14	CTCF	chr15:78365080-78365230	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr15:78365160-78365310	HBMEC	blood vessel:	n/a	n/a
16	CTCF	chr15:78365080-78365230	AG09319	gingival:	n/a	n/a
17	CTCF	chr15:78365200-78365350	AG10803	skin:	n/a	n/a
18	CTCF	chr15:78365120-78365270	HCFaa	heart:	n/a	n/a
19	CTCF	chr15:78365120-78365270	HMF	breast:	n/a	n/a
20	CTCF	chr15:78365160-78365310	HPAF	blood vessel:	n/a	n/a
21	USF2	chr15:78364921-78365404	HepG2	liver:	n/a	n/a
22	POLR2A	chr15:78364789-78365363	HL-60	blood:	n/a	n/a
23	CTCF	chr15:78365180-78365330	HRPEpiC	eye:	n/a	n/a
24	MAX	chr15:78364767-78365346	NB4	blood:	n/a	n/a
25	CREB1	chr15:78364802-78365284	HepG2	liver:	n/a	n/a
26	CTCF	chr15:78365120-78365270	HBMEC	blood vessel:	n/a	n/a
27	USF1	chr15:78364939-78365222	HepG2	liver:	n/a	chr15:78365104-78365115

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78362996..78365897-chr15:78366671..78369435,4	MCF-7	breast:
2	chr15:78354448..78356062-chr15:78363127..78365544,2	K562	blood:

No data

Variant related genes	Relation type
SH2D7	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1004855	0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs10519181	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs11072716	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11631578	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11634607	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs11638311	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11852768	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12148365	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs12442213	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs12591418	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs12594823	0.86[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs12899061	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12907701	0.95[ASN][1000 genomes]
rs12907814	0.96[ASN][1000 genomes]
rs12911332	0.90[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap]
rs12916362	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1348257	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs1442293	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1837913	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1992470	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2028546	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2044099	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs2241885	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2867985	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs2903702	0.99[ASN][1000 genomes]
rs3803380	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs4395040	0.91[CHB][hapmap];0.93[CHD][hapmap]
rs4886553	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4886554	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs4886555	0.96[ASN][1000 genomes]
rs4886994	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4886995	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs4886996	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4886999	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4887000	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56317829	0.94[ASN][1000 genomes]
rs57220134	0.95[ASN][1000 genomes]
rs58578288	0.96[ASN][1000 genomes]
rs62011511	0.96[ASN][1000 genomes]
rs67559383	0.87[AFR][1000 genomes]
rs7166819	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170746	0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs7173128	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7174489	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7181594	0.98[ASN][1000 genomes]
rs8029562	0.92[ASN][1000 genomes]
rs8030873	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9047	0.96[ASN][1000 genomes]

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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12901812	ISL2	cis	parietal	SCAN
rs12901812	CLK3	cis	cerebellum	SCAN
rs12901812	HEXA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78347400-78367800	Enhancers	Placenta	Placenta
2	chr15:78354200-78366400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:78354600-78365400	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr15:78354600-78366400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr15:78355600-78365400	Enhancers	Small Intestine	intestine
6	chr15:78358400-78366000	Enhancers	HepG2	liver
7	chr15:78358800-78367800	Weak transcription	HMEC	breast
8	chr15:78361400-78367800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:78361400-78368000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:78361400-78368000	Weak transcription	Fetal Heart	heart
11	chr15:78361400-78368200	Weak transcription	Brain Germinal Matrix	brain
12	chr15:78361600-78365400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr15:78361600-78369200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:78362000-78366000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr15:78362600-78365600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:78362600-78365600	Enhancers	Thymus	Thymus
17	chr15:78362800-78368000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:78362800-78368000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr15:78362800-78368000	Weak transcription	Esophagus	oesophagus
20	chr15:78362800-78369200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:78363000-78368000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:78363000-78368000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr15:78363200-78367200	Weak transcription	Stomach Mucosa	stomach
24	chr15:78363200-78368000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:78363400-78366200	Enhancers	Fetal Intestine Small	intestine
26	chr15:78363600-78365600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:78363600-78366000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:78363600-78366200	Enhancers	HSMM	muscle
29	chr15:78363600-78366200	Enhancers	NHLF	lung
30	chr15:78363600-78367800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr15:78363800-78365400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr15:78363800-78365600	Enhancers	NH-A	brain
33	chr15:78363800-78366000	Enhancers	Primary hematopoietic stem cells	blood
34	chr15:78364000-78365400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr15:78364000-78365400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr15:78364000-78365400	Enhancers	Pancreas	Pancrea
37	chr15:78364000-78365400	Enhancers	Spleen	Spleen
38	chr15:78364000-78365800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:78364200-78365400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:78364200-78365400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:78364200-78365400	Enhancers	Brain Angular Gyrus	brain
42	chr15:78364200-78365600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:78364200-78365600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr15:78364200-78365600	Enhancers	Brain Cingulate Gyrus	brain
45	chr15:78364200-78365600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr15:78364400-78365400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:78364400-78365400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:78364400-78365400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:78364400-78365400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:78364400-78365400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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