Variant report

Variant	rs5009711
Chromosome Location	chr6:25333090-25333091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25331246..25333492-chr6:25335317..25337907,2	K562	blood:
2	chr6:25326407..25328243-chr6:25331824..25333958,2	MCF-7	breast:
3	chr6:25278190..25281411-chr6:25333036..25336793,4	MCF-7	breast:
4	chr6:25270434..25272961-chr6:25332945..25335703,2	K562	blood:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10456321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192665	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192812	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192951	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196438	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34247480	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5009712	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5009714	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555189	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555190	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555191	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555192	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555193	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555194	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760865	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746360	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746606	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752550	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762836	1.00[CHD][hapmap]
rs7770388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5009711	HIST1H2AC	cis	cerebellum	SCAN
rs5009711	FAM65B	cis	parietal	SCAN
rs5009711	HIST1H2BE	cis	cerebellum	SCAN
rs5009711	PRSS16	cis	cerebellum	SCAN

Chromatin state (count:80 , 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	chr6:25323000-25333200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:25325200-25336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:25325200-25336400	Weak transcription	Lung	lung
5	chr6:25327600-25337400	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:25328200-25336800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:25328200-25338200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr6:25329000-25336000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:25329400-25336200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:25329400-25336400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:25329600-25336400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:25330000-25335200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:25330200-25335000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:25330400-25337200	Weak transcription	Brain Substantia Nigra	brain
15	chr6:25330600-25335800	Weak transcription	Esophagus	oesophagus
16	chr6:25330600-25335800	Weak transcription	Gastric	stomach
17	chr6:25331000-25335800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:25331000-25336000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr6:25331200-25335600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:25331200-25336800	Enhancers	Right Atrium	heart
21	chr6:25331400-25333400	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:25331400-25333400	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:25331400-25333800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:25331400-25335000	Weak transcription	Primary T cells from cord blood	blood
25	chr6:25331400-25335400	Enhancers	Stomach Mucosa	stomach
26	chr6:25331400-25336600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:25331600-25333400	Enhancers	Adipose Nuclei	Adipose
28	chr6:25331800-25336400	Weak transcription	Pancreas	Pancrea
29	chr6:25331800-25341800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:25332000-25333200	Weak transcription	Fetal Intestine Small	intestine
31	chr6:25332000-25333800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:25332000-25334000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:25332000-25334000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:25332000-25336200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:25332000-25336200	Weak transcription	NHEK	skin
36	chr6:25332000-25336600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:25332000-25336600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:25332000-25337200	Weak transcription	Fetal Brain Female	brain
39	chr6:25332000-25337400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:25332000-25337800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:25332000-25342400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:25332000-25342600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:25332000-25342600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr6:25332000-25346800	Weak transcription	Ovary	ovary
45	chr6:25332200-25334200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:25332200-25337600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:25332400-25333400	Enhancers	GM12878-XiMat	blood
48	chr6:25332400-25333600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr6:25332400-25333600	Weak transcription	Small Intestine	intestine
50	chr6:25332400-25334400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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