Variant report

Variant	rs6914799
Chromosome Location	chr6:25280119-25280120
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52312108..52312672-chr6:25279463..25280301,2	Hela-S3	cervix:
2	chr10:101491868..101492807-chr6:25279651..25280618,2	Hela-S3	cervix:
3	chr6:25201388..25203909-chr6:25279159..25280911,2	MCF-7	breast:
4	chr6:25277929..25281528-chr6:25281560..25287992,8	MCF-7	breast:
5	chr6:25277697..25280622-chr6:25286931..25288666,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119929	Chromatin interaction
ENSG00000264238	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000207286	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1016854	0.88[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs1016855	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018839	0.82[CHD][hapmap]
rs2050044	0.87[EUR][1000 genomes]
rs2064211	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2078527	0.88[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs2690054	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2690064	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2690134	0.82[CHD][hapmap]
rs2744257	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.87[ASN][1000 genomes]
rs2744258	0.87[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs2744267	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2744269	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744288	0.82[CHD][hapmap]
rs2744294	0.82[CHD][hapmap]
rs6908902	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909014	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926126	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721036	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs721037	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs723047	0.89[EUR][1000 genomes]
rs723048	0.91[CEU][hapmap];0.95[ASN][1000 genomes]
rs7748256	0.85[EUR][1000 genomes]
rs9356971	0.85[EUR][1000 genomes]
rs9356972	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs9358848	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9358849	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs9366614	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9379746	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9379747	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9379750	0.88[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs9393636	0.84[EUR][1000 genomes]
rs9393637	0.88[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
rs6914799	HIST1H3B	cis	cerebellum	SCAN
rs6914799	HIST1H4L	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25278400-25280800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25278400-25281600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:25278400-25281600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:25278400-25281600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:25278600-25280200	Flanking Bivalent TSS/Enh	Dnd41	blood
6	chr6:25278600-25280400	Active TSS	Brain Germinal Matrix	brain
7	chr6:25278600-25280600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:25278600-25281000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:25278600-25281000	Active TSS	A549	lung
10	chr6:25278600-25281200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:25278600-25281400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr6:25278600-25281400	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr6:25278600-25281400	Active TSS	Right Ventricle	heart
14	chr6:25278600-25283400	Active TSS	Aorta	Aorta
15	chr6:25278800-25280200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:25278800-25280400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:25278800-25280400	Active TSS	Stomach Mucosa	stomach
18	chr6:25278800-25280600	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:25278800-25280600	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr6:25278800-25280800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:25278800-25280800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr6:25278800-25281000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:25278800-25281000	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr6:25278800-25281000	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:25278800-25281000	Active TSS	Placenta Amnion	Placenta Amnion
26	chr6:25278800-25281200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:25278800-25281200	Active TSS	Esophagus	oesophagus
28	chr6:25278800-25281200	Active TSS	Ovary	ovary
29	chr6:25278800-25281400	Active TSS	Fetal Kidney	kidney
30	chr6:25278800-25281600	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr6:25278800-25281600	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:25278800-25281600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:25278800-25281600	Active TSS	Right Atrium	heart
34	chr6:25279000-25280200	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr6:25279000-25280200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:25279000-25280200	Active TSS	Psoas Muscle	Psoas
37	chr6:25279000-25280200	Active TSS	Rectal Smooth Muscle	rectum
38	chr6:25279000-25280600	Active TSS	HMEC	breast
39	chr6:25279000-25280800	Active TSS	Colon Smooth Muscle	Colon
40	chr6:25279000-25280800	Active TSS	Fetal Lung	lung
41	chr6:25279000-25280800	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr6:25279000-25280800	Active TSS	Hela-S3	cervix
43	chr6:25279000-25280800	Active TSS	HSMM	muscle
44	chr6:25279000-25281000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:25279000-25281000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:25279000-25281000	Active TSS	Pancreas	Pancrea
47	chr6:25279000-25281000	Active TSS	Small Intestine	intestine
48	chr6:25279000-25281000	Active TSS	NHDF-Ad	bronchial
49	chr6:25279000-25281200	Active TSS	Gastric	stomach
50	chr6:25279000-25281400	Active TSS	Fetal Intestine Small	intestine

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