Variant report

Variant	rs11638663
Chromosome Location	chr15:75950163-75950164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75930676..75935484-chr15:75948921..75956484,11	MCF-7	breast:
2	chr15:75815715..75817724-chr15:75948074..75950667,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177971	Chromatin interaction
ENSG00000169410	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11547316	1.00[CHD][hapmap]
rs11632887	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11634828	1.00[CHD][hapmap]
rs11635996	1.00[CHD][hapmap]
rs11637785	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11856001	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62027227	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62027229	0.84[EUR][1000 genomes]
rs62027230	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62027233	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8031394	0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
7	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
10	nsv904391	chr15:75930757-76001654	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
12	nsv904393	chr15:75932177-76001654	Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	nsv984485	chr15:75932760-75965433	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11638663	NRG4	cis	parietal	SCAN
rs11638663	SNX33	cis	cerebellum	SCAN
rs11638663	MAN2C1	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75941800-75953200	Weak transcription	Fetal Brain Female	brain
2	chr15:75943800-75952800	Weak transcription	Fetal Kidney	kidney
3	chr15:75944000-75951800	Weak transcription	Brain Angular Gyrus	brain
4	chr15:75944200-75952000	Weak transcription	HSMMtube	muscle
5	chr15:75944400-75952400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:75944600-75954400	Genic enhancers	Lung	lung
7	chr15:75944800-75953800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:75945000-75952200	Weak transcription	Thymus	Thymus
9	chr15:75945000-75953000	Weak transcription	HUVEC	blood vessel
10	chr15:75945000-75954000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:75945000-75954400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:75945200-75953000	Weak transcription	Fetal Brain Male	brain
13	chr15:75945200-75955000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:75945400-75953000	Weak transcription	Fetal Thymus	thymus
15	chr15:75945600-75951800	Weak transcription	A549	lung
16	chr15:75945600-75953000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:75945800-75951200	Weak transcription	Psoas Muscle	Psoas
18	chr15:75945800-75951800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:75945800-75952000	Weak transcription	Brain Substantia Nigra	brain
20	chr15:75945800-75952800	Weak transcription	Small Intestine	intestine
21	chr15:75946000-75950200	Weak transcription	Brain Germinal Matrix	brain
22	chr15:75946000-75952400	Weak transcription	NH-A	brain
23	chr15:75946000-75953200	Genic enhancers	Pancreas	Pancrea
24	chr15:75946000-75953400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:75946200-75952600	Strong transcription	Fetal Stomach	stomach
26	chr15:75946200-75952800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:75946200-75953000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:75946600-75952600	Strong transcription	Osteobl	bone
29	chr15:75946800-75951400	Weak transcription	HSMM	muscle
30	chr15:75946800-75952800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:75946800-75956600	Weak transcription	K562	blood
32	chr15:75947200-75951600	Strong transcription	NHLF	lung
33	chr15:75947200-75955200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:75947400-75952000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr15:75947600-75951000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:75947600-75951800	Strong transcription	Placenta	Placenta
37	chr15:75947600-75952400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:75947800-75950800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr15:75947800-75951400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:75947800-75951800	Strong transcription	Ovary	ovary
41	chr15:75947800-75952200	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:75947800-75952400	Strong transcription	Gastric	stomach
43	chr15:75947800-75952800	Strong transcription	Left Ventricle	heart
44	chr15:75947800-75953200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:75948000-75950800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr15:75948000-75951400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:75948000-75951400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:75948000-75951400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:75948000-75951600	Weak transcription	NHDF-Ad	bronchial
50	chr15:75948000-75952000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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