Variant report

Variant	rs7762537
Chromosome Location	chr6:25334967-25334968
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25278959..25280909-chr6:25333300..25336111,2	MCF-7	breast:
2	chr6:25278190..25281411-chr6:25333036..25336793,4	MCF-7	breast:
3	chr6:25270434..25272961-chr6:25332945..25335703,2	K562	blood:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11752017	1.00[JPT][hapmap]
rs11759560	1.00[JPT][hapmap]
rs11759648	1.00[JPT][hapmap]
rs12203031	1.00[JPT][hapmap]
rs12203442	1.00[JPT][hapmap]
rs12211739	1.00[JPT][hapmap]
rs184202	1.00[JPT][hapmap]
rs212927	1.00[JPT][hapmap]
rs212939	1.00[JPT][hapmap]
rs212940	1.00[JPT][hapmap]
rs301377	1.00[JPT][hapmap]
rs441472	1.00[JPT][hapmap]
rs453181	1.00[JPT][hapmap]
rs485567	1.00[JPT][hapmap]
rs55896906	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716796	1.00[JPT][hapmap]
rs760865	1.00[JPT][hapmap]
rs7752524	1.00[JPT][hapmap]
rs7762821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762836	0.81[MEX][hapmap]
rs7764258	1.00[JPT][hapmap]
rs9461151	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7762537	HIST1H2BL	cis	cerebellum	SCAN
rs7762537	HIST1H2BI	cis	parietal	SCAN
rs7762537	NRSN1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25321600-25341200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:25325200-25336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:25325200-25336400	Weak transcription	Lung	lung
4	chr6:25327600-25337400	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:25328200-25336800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:25328200-25338200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:25329000-25336000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:25329400-25336200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:25329400-25336400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:25329600-25336400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:25330000-25335200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:25330200-25335000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:25330400-25337200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:25330600-25335800	Weak transcription	Esophagus	oesophagus
15	chr6:25330600-25335800	Weak transcription	Gastric	stomach
16	chr6:25331000-25335800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:25331000-25336000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:25331200-25335600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:25331200-25336800	Enhancers	Right Atrium	heart
20	chr6:25331400-25335000	Weak transcription	Primary T cells from cord blood	blood
21	chr6:25331400-25335400	Enhancers	Stomach Mucosa	stomach
22	chr6:25331400-25336600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr6:25331800-25336400	Weak transcription	Pancreas	Pancrea
24	chr6:25331800-25341800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:25332000-25336200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:25332000-25336200	Weak transcription	NHEK	skin
27	chr6:25332000-25336600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:25332000-25336600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:25332000-25337200	Weak transcription	Fetal Brain Female	brain
30	chr6:25332000-25337400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:25332000-25337800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:25332000-25342400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:25332000-25342600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:25332000-25342600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:25332000-25346800	Weak transcription	Ovary	ovary
36	chr6:25332200-25337600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:25332600-25336400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:25332600-25336800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr6:25332600-25339800	Weak transcription	Colonic Mucosa	Colon
40	chr6:25332800-25335200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr6:25332800-25337200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:25332800-25341200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:25333200-25343800	Enhancers	Fetal Intestine Small	intestine
44	chr6:25333400-25335000	Weak transcription	GM12878-XiMat	blood
45	chr6:25333400-25335200	Weak transcription	Adipose Nuclei	Adipose
46	chr6:25333400-25336400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:25333400-25337600	Weak transcription	Brain Angular Gyrus	brain
48	chr6:25333400-25340800	Weak transcription	Aorta	Aorta
49	chr6:25333800-25336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:25333800-25336600	Weak transcription	Rectal Mucosa Donor 29	rectum

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