Variant report

Variant	rs7748771
Chromosome Location	chr6:25355099-25355100
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25279234..25281745-chr6:25353189..25355641,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11967836	1.00[CEU][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs17251430	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs17316893	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs1883392	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149227	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs56930318	0.91[EUR][1000 genomes]
rs57899991	0.91[EUR][1000 genomes]
rs59821513	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60982159	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456671	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6905765	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73383424	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73399971	0.91[EUR][1000 genomes]
rs7749494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750545	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763072	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9461142	0.91[EUR][1000 genomes]
rs9467477	0.82[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985984	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs9986335	0.91[EUR][1000 genomes]
rs9986608	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7748771	HIST1H2AE	cis	lymphoblastoid	seeQTL
rs7748771	HIST1H2AD	cis	lymphoblastoid	seeQTL
rs7748771	ARMCX5	trans	lymphoblastoid	seeQTL
rs7748771	DSG2	trans	lymphoblastoid	seeQTL
rs7748771	HIST1H3D	cis	lymphoblastoid	seeQTL
rs7748771	HIST1H2BC	cis	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
2	chr6:25337400-25357800	Weak transcription	NHEK	skin
3	chr6:25341000-25359400	Weak transcription	Pancreas	Pancrea
4	chr6:25346600-25359400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:25346800-25359200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:25347000-25359400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:25349200-25359200	Weak transcription	Ovary	ovary
8	chr6:25350400-25355200	Enhancers	Fetal Lung	lung
9	chr6:25350600-25356000	Enhancers	Fetal Intestine Large	intestine
10	chr6:25350800-25359200	Weak transcription	Lung	lung
11	chr6:25351000-25359600	Weak transcription	Brain Anterior Caudate	brain
12	chr6:25351200-25357400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:25351800-25359200	Weak transcription	HSMMtube	muscle
14	chr6:25352200-25363000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr6:25353000-25359400	Weak transcription	Fetal Thymus	thymus
16	chr6:25353200-25359600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:25353200-25359600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:25353400-25358200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:25353400-25358800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:25353400-25359200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:25353400-25359200	Weak transcription	Small Intestine	intestine
22	chr6:25353800-25357400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:25353800-25359400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:25354200-25355400	Enhancers	Fetal Heart	heart
25	chr6:25354200-25355400	Enhancers	Stomach Mucosa	stomach
26	chr6:25354200-25355800	Enhancers	Aorta	Aorta
27	chr6:25354400-25355200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:25354400-25355200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:25354400-25355600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:25354600-25355200	Enhancers	Right Atrium	heart
31	chr6:25354600-25355200	Enhancers	NHDF-Ad	bronchial
32	chr6:25354600-25355400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:25354600-25355400	Enhancers	Fetal Muscle Leg	muscle
34	chr6:25354600-25355400	Enhancers	NHLF	lung
35	chr6:25354600-25355600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:25354600-25356000	Enhancers	Fetal Intestine Small	intestine
37	chr6:25354600-25359400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:25354800-25355200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:25354800-25355200	Enhancers	Osteobl	bone
40	chr6:25355000-25355200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:25355000-25356000	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr6:25355000-25359200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:25355000-25359200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:25355000-25359200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:25355000-25359400	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links