Variant report

Variant	rs7764258
Chromosome Location	chr6:25322814-25322815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25302209..25304566-chr6:25321319..25323421,2	MCF-7	breast:
2	chr6:25315748..25318380-chr6:25321578..25323806,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10456320	0.83[LWK][hapmap];1.00[YRI][hapmap]
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]
rs17678510	1.00[CHD][hapmap]
rs184202	1.00[JPT][hapmap]
rs2018839	0.94[LWK][hapmap]
rs212939	1.00[JPT][hapmap]
rs2690110	0.88[LWK][hapmap]
rs2690113	0.90[ASN][1000 genomes]
rs2744294	0.88[LWK][hapmap]
rs301377	1.00[JPT][hapmap]
rs441472	1.00[JPT][hapmap]
rs453181	1.00[JPT][hapmap]
rs4712910	0.85[YRI][hapmap]
rs6902634	1.00[YRI][hapmap]
rs716796	1.00[JPT][hapmap]
rs760865	1.00[JPT][hapmap]
rs7743997	1.00[YRI][hapmap]
rs7752524	1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7762537	1.00[JPT][hapmap]
rs7767189	1.00[YRI][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7764258	HIST1H2BL	cis	parietal	SCAN
rs7764258	PRRX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
2	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
3	chr6:25312000-25324200	Weak transcription	Esophagus	oesophagus
4	chr6:25312000-25324200	Weak transcription	Pancreas	Pancrea
5	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:25313800-25325800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:25313800-25326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:25314000-25325000	Weak transcription	Placenta	Placenta
10	chr6:25315400-25329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:25315800-25324200	Weak transcription	Hela-S3	cervix
12	chr6:25316200-25326800	Weak transcription	Gastric	stomach
13	chr6:25316400-25326600	Weak transcription	Fetal Kidney	kidney
14	chr6:25316600-25324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:25317200-25324200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:25317200-25324200	Weak transcription	Aorta	Aorta
17	chr6:25317400-25324000	Weak transcription	Fetal Intestine Large	intestine
18	chr6:25318600-25324200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:25318600-25324400	Weak transcription	Lung	lung
20	chr6:25319000-25324200	Weak transcription	Ovary	ovary
21	chr6:25319000-25324200	Weak transcription	Right Atrium	heart
22	chr6:25319200-25324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:25319400-25324200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:25319400-25324200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:25319800-25324200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:25320600-25324200	Weak transcription	Fetal Intestine Small	intestine
27	chr6:25321000-25324200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:25321000-25324200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:25321000-25324200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:25321000-25324200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:25321000-25324200	Weak transcription	A549	lung
32	chr6:25321000-25324200	Weak transcription	Osteobl	bone
33	chr6:25321000-25324400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:25321000-25329400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:25321000-25329600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:25321000-25331400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:25321200-25324000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:25321200-25324200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:25321200-25326000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:25321200-25329200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:25321200-25329400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:25321200-25329400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:25321600-25324200	Weak transcription	HSMMtube	muscle
44	chr6:25321600-25324400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:25321600-25325200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:25321600-25329200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:25321600-25329400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:25321600-25329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:25321600-25329800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:25321600-25341200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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