Variant report

Variant	rs7762836
Chromosome Location	chr6:25335121-25335122
allele	C/T
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMAHP-6	chr6:25335059-25335464	NONHSAT108154

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12192951	1.00[CHD][hapmap]
rs5009711	1.00[CHD][hapmap]
rs5009712	1.00[CHD][hapmap]
rs7746360	1.00[CHD][hapmap]
rs7762537	0.81[MEX][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7762836	HIST1H2AG	cis	cerebellum	SCAN
rs7762836	HIST1H2AE	cis	cerebellum	SCAN
rs7762836	HIST1H2BE	cis	cerebellum	SCAN
rs7762836	HIST1H3E	cis	parietal	SCAN
rs7762836	PRSS16	cis	cerebellum	SCAN
rs7762836	HIST1H2AC	cis	cerebellum	SCAN

Chromatin state (count:70 , 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	chr6:25330400-25337200	Weak transcription	Brain Substantia Nigra	brain
13	chr6:25330600-25335800	Weak transcription	Esophagus	oesophagus
14	chr6:25330600-25335800	Weak transcription	Gastric	stomach
15	chr6:25331000-25335800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:25331000-25336000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:25331200-25335600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:25331200-25336800	Enhancers	Right Atrium	heart
19	chr6:25331400-25335400	Enhancers	Stomach Mucosa	stomach
20	chr6:25331400-25336600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:25331800-25336400	Weak transcription	Pancreas	Pancrea
22	chr6:25331800-25341800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:25332000-25336200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:25332000-25336200	Weak transcription	NHEK	skin
25	chr6:25332000-25336600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:25332000-25336600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:25332000-25337200	Weak transcription	Fetal Brain Female	brain
28	chr6:25332000-25337400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:25332000-25337800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:25332000-25342400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:25332000-25342600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:25332000-25342600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:25332000-25346800	Weak transcription	Ovary	ovary
34	chr6:25332200-25337600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:25332600-25336400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:25332600-25336800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr6:25332600-25339800	Weak transcription	Colonic Mucosa	Colon
38	chr6:25332800-25335200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr6:25332800-25337200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:25332800-25341200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:25333200-25343800	Enhancers	Fetal Intestine Small	intestine
42	chr6:25333400-25335200	Weak transcription	Adipose Nuclei	Adipose
43	chr6:25333400-25336400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:25333400-25337600	Weak transcription	Brain Angular Gyrus	brain
45	chr6:25333400-25340800	Weak transcription	Aorta	Aorta
46	chr6:25333800-25336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:25333800-25336600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr6:25333800-25337000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:25333800-25346400	Weak transcription	Left Ventricle	heart
50	chr6:25334200-25335600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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