Variant report

Variant	rs11636613
Chromosome Location	chr15:77335902-77335903
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	RCOR1	chr15:77335800-77335930	K562	blood:	n/a	n/a
2	POLR2A	chr15:77335799-77335937	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:77335660-77336401	HL-60	blood:	n/a	n/a
4	POLR2A	chr15:77333901-77336487	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77334649..77338471-chr15:77361377..77364899,5	K562	blood:
2	chr15:77334559..77338244-chr15:77361377..77364599,4	K562	blood:

Variant related genes	Relation type
ENSG00000259652	TF binding region
ENSG00000260787	TF binding region
ENSG00000140391	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11072641	0.85[AMR][1000 genomes]
rs11630497	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636648	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11737	0.94[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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12148761	0.96[CEU][hapmap]
rs12372961	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[ASN][1000 genomes]
rs12901188	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12912792	0.81[ASN][1000 genomes]
rs16968665	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs2404233	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs2404234	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[ASN][1000 genomes]
rs34443712	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3935339	0.87[JPT][hapmap]
rs4078354	0.87[CEU][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap]
rs4886509	0.94[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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886847	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[ASN][1000 genomes]
rs55645420	0.81[ASN][1000 genomes]
rs7166154	0.96[CEU][hapmap]
rs7169831	1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs7177533	0.81[CHB][hapmap]
rs8032	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9806416	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1048833	chr15:77294593-77339260	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv511547	chr15:77328269-77337649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11636613	RP11-797A18.4	cis	Esophagus Muscularis	GTEx
rs11636613	PSTPIP1	cis	lymphoblastoid	seeQTL
rs11636613	ISL2	cis	cerebellum	SCAN
rs11636613	TSPAN3	cis	cerebellum	SCAN
rs11636613	RP11-797A18.4	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77318400-77350600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:77321200-77362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:77323000-77336000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:77323400-77346000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:77326800-77349800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:77327400-77336400	Weak transcription	Psoas Muscle	Psoas
7	chr15:77327400-77346000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:77327600-77338000	Weak transcription	NHDF-Ad	bronchial
9	chr15:77327800-77346800	Strong transcription	Primary B cells from cord blood	blood
10	chr15:77328000-77338600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:77328000-77344400	Weak transcription	Small Intestine	intestine
12	chr15:77328400-77336000	Strong transcription	Stomach Smooth Muscle	stomach
13	chr15:77328600-77336000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:77328600-77336400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr15:77328600-77337400	Weak transcription	Brain Substantia Nigra	brain
16	chr15:77329600-77336600	Weak transcription	Esophagus	oesophagus
17	chr15:77329600-77339600	Strong transcription	Primary hematopoietic stem cells	blood
18	chr15:77329800-77336000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:77330000-77337000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:77330000-77338800	Weak transcription	Aorta	Aorta
21	chr15:77330000-77352000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr15:77330000-77352200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:77330200-77336000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:77330200-77336200	Weak transcription	NHLF	lung
25	chr15:77330200-77337000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:77330200-77352400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr15:77330400-77336000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr15:77330400-77336400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:77330400-77336800	Weak transcription	GM12878-XiMat	blood
30	chr15:77330400-77338000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:77330600-77336400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:77330600-77337000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:77330600-77337800	Strong transcription	Fetal Thymus	thymus
34	chr15:77330600-77350200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:77330800-77339400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:77331000-77336000	Weak transcription	Fetal Brain Male	brain
37	chr15:77331000-77337600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:77331200-77345600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:77331600-77339600	Strong transcription	Fetal Intestine Small	intestine
40	chr15:77332000-77338200	Weak transcription	Stomach Mucosa	stomach
41	chr15:77332400-77340000	Strong transcription	Fetal Intestine Large	intestine
42	chr15:77332400-77340000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr15:77332800-77336800	Strong transcription	Fetal Muscle Leg	muscle
44	chr15:77332800-77336800	Strong transcription	Lung	lung
45	chr15:77332800-77339800	Strong transcription	Fetal Stomach	stomach
46	chr15:77332800-77344400	Weak transcription	K562	blood
47	chr15:77333000-77336000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr15:77333000-77339600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:77333000-77342800	Strong transcription	A549	lung
50	chr15:77333200-77339800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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