Variant report

Variant	rs11604662
Chromosome Location	chr11:67268048-67268049
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	chr11:67267656-67268060	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:67267742-67268240	GM12878	blood:	n/a	n/a
3	NFIC	chr11:67267972-67268890	ECC-1	luminal epithelium:	n/a	chr11:67268480-67268496 chr11:67268182-67268199 chr11:67268470-67268498 chr11:67268480-67268497
4	POLR2A	chr11:67267404-67268085	K562	blood:	n/a	n/a
5	POLR2A	chr11:67267084-67268162	A549	lung:	n/a	n/a
6	POLR2A	chr11:67267736-67268107	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:67267689-67268153	K562	blood:	n/a	n/a
8	POLR2A	chr11:67267059-67268291	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr11:67267270-67268102	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:67249113..67250802-chr11:67267518..67269287,2	MCF-7	breast:
2	chr11:67266460..67268680-chr11:67274631..67276596,2	MCF-7	breast:
3	chr11:67263850..67266105-chr11:67266792..67269183,3	MCF-7	breast:
4	chr11:67161312..67163125-chr11:67265626..67268296,2	MCF-7	breast:

Variant related genes	Relation type
PITPNM1	TF binding region
ENSG00000110711	Chromatin interaction
ENSG00000167797	Chromatin interaction
ENSG00000253024	Chromatin interaction
ENSG00000110697	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17501521	0.91[CEU][hapmap];0.88[TSI][hapmap]
rs4465371	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs7936800	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv897797	chr11:67023040-67293234	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
3	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
5	esv1818769	chr11:67138811-67300457	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
6	esv1798859	chr11:67139954-67272983	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
7	nsv897805	chr11:67155210-67283891	ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
8	nsv897806	chr11:67155210-67294308	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
9	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
10	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
11	nsv897809	chr11:67156875-67276235	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
12	nsv555254	chr11:67164495-67288594	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
13	nsv534229	chr11:67164667-67411909	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
14	nsv897813	chr11:67175692-67283891	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription 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	132 gene(s)	inside rSNPs	diseases
15	nsv521723	chr11:67175692-67311258	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
16	nsv468604	chr11:67186000-67283891	Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
17	nsv555256	chr11:67186000-67283891	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
18	nsv527056	chr11:67207426-67294308	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases
19	esv2422195	chr11:67234322-67626901	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Weak transcription 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 miRNA target site	146 gene(s)	inside rSNPs	diseases
20	nsv1052919	chr11:67252337-67306030	Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
21	nsv541078	chr11:67252337-67306030	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11604662	PTPRCAP	cis	Nerve Tibial	GTEx
rs11604662	RTN3	cis	parietal	SCAN
rs11604662	CABP2	cis	parietal	SCAN
rs11604662	ATG2A	cis	parietal	SCAN
rs11604662	GSTP1	cis	cerebellum	SCAN
rs11604662	TBC1D10C	cis	parietal	SCAN
rs11604662	GSTP1	cis	parietal	SCAN
rs11604662	NDUFV1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67251000-67271000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:67251400-67271200	Weak transcription	HSMM	muscle
3	chr11:67251400-67271400	Weak transcription	HUVEC	blood vessel
4	chr11:67251600-67268400	Weak transcription	NH-A	brain
5	chr11:67251600-67268600	Strong transcription	Fetal Intestine Small	intestine
6	chr11:67251600-67270600	Weak transcription	Fetal Heart	heart
7	chr11:67251600-67271400	Weak transcription	NHDF-Ad	bronchial
8	chr11:67252600-67270000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:67252600-67270200	Strong transcription	Fetal Stomach	stomach
10	chr11:67252600-67271600	Weak transcription	Psoas Muscle	Psoas
11	chr11:67252800-67270000	Weak transcription	Fetal Brain Male	brain
12	chr11:67252800-67271400	Weak transcription	Right Atrium	heart
13	chr11:67253800-67269600	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:67254000-67270000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:67254000-67270800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:67254000-67271000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:67254200-67268600	Strong transcription	Gastric	stomach
18	chr11:67254400-67270600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:67254400-67271200	Weak transcription	K562	blood
20	chr11:67254600-67270600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:67254800-67270800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr11:67254800-67271000	Weak transcription	HepG2	liver
23	chr11:67255800-67270200	Strong transcription	Dnd41	blood
24	chr11:67255800-67272000	Weak transcription	Fetal Kidney	kidney
25	chr11:67256000-67270400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr11:67256400-67270800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:67256600-67270200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr11:67256600-67270400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:67256600-67270600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:67257000-67270200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr11:67257400-67269800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:67257400-67270800	Strong transcription	Fetal Thymus	thymus
33	chr11:67257400-67270800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:67257600-67270200	Strong transcription	Colonic Mucosa	Colon
35	chr11:67257600-67270600	Weak transcription	Stomach Mucosa	stomach
36	chr11:67257600-67271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:67257800-67271200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:67258000-67270600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:67258000-67270800	Weak transcription	HMEC	breast
40	chr11:67258000-67271200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:67258200-67269800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr11:67258400-67270200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr11:67259000-67268400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:67259000-67268400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:67259000-67268800	Strong transcription	A549	lung
46	chr11:67259400-67270000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:67259600-67270400	Strong transcription	Placenta	Placenta
48	chr11:67259800-67271200	Weak transcription	Ovary	ovary
49	chr11:67260000-67270200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:67260000-67271000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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