Variant report

Variant	rs2235397
Chromosome Location	chr6:11762774-11762775
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	chr6:11761684..11763323-chr6:12010359..12013235,2	K562	blood:
2	chr6:11760325..11763713-chr6:11770760..11773174,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095951	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12189748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12198491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12211506	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs210890	0.81[CEU][hapmap]
rs210925	0.85[CHB][hapmap]
rs210926	0.81[CEU][hapmap]
rs210931	0.81[CEU][hapmap]
rs2235396	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2743953	0.81[CEU][hapmap]
rs2781127	0.81[CEU][hapmap]
rs4713852	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457810	0.81[CEU][hapmap]
rs6457825	0.85[CHB][hapmap]
rs6908760	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6911562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6938865	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs9368866	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs9380503	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9394295	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9462058	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9469947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9469963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2235397	C6orf105	Cis_1M	lymphoblastoid	RTeQTL
rs2235397	CYP2E1	trans	parietal	SCAN
rs2235397	SLC35B3	cis	parietal	SCAN
rs2235397	ERVFRDE1	cis	parietal	SCAN
rs2235397	TBC1D7	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11753200-11763800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:11755800-11768400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:11759000-11765800	Enhancers	Fetal Intestine Large	intestine
4	chr6:11759200-11764400	Enhancers	Stomach Mucosa	stomach
5	chr6:11759200-11765600	Enhancers	Fetal Intestine Small	intestine
6	chr6:11759400-11763600	Weak transcription	Esophagus	oesophagus
7	chr6:11759400-11769600	Weak transcription	Lung	lung
8	chr6:11759600-11763400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:11759600-11765000	Enhancers	Duodenum Mucosa	Duodenum
10	chr6:11759600-11765800	Weak transcription	Hela-S3	cervix
11	chr6:11759800-11764400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:11760000-11763400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:11760400-11765800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:11760600-11762800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:11760600-11763600	Weak transcription	Ovary	ovary
16	chr6:11760600-11763600	Weak transcription	Right Atrium	heart
17	chr6:11760600-11766000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:11760600-11770600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:11760800-11763600	Weak transcription	Small Intestine	intestine
20	chr6:11761000-11763200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:11761400-11762800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr6:11761600-11765800	Weak transcription	K562	blood
23	chr6:11762000-11762800	Enhancers	Pancreas	Pancrea
24	chr6:11762000-11764400	Enhancers	NHEK	skin
25	chr6:11762000-11764600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:11762000-11767200	Enhancers	HSMMtube	muscle
27	chr6:11762200-11763600	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:11762200-11763800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:11762200-11764000	Enhancers	Fetal Kidney	kidney
30	chr6:11762200-11764400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr6:11762200-11764600	Enhancers	Fetal Lung	lung
32	chr6:11762200-11764600	Enhancers	NH-A	brain
33	chr6:11762400-11763200	Enhancers	Fetal Heart	heart
34	chr6:11762400-11763600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr6:11762400-11763600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:11762400-11763800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:11762400-11764000	Enhancers	Osteobl	bone
38	chr6:11762400-11764400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:11762400-11764400	Enhancers	HSMM	muscle
40	chr6:11762400-11764600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:11762400-11764600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:11762400-11765400	Enhancers	Aorta	Aorta
43	chr6:11762400-11768200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:11762600-11762800	Weak transcription	Colonic Mucosa	Colon
45	chr6:11762600-11762800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr6:11762600-11762800	Enhancers	A549	lung
47	chr6:11762600-11763000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:11762600-11763000	Weak transcription	HMEC	breast
49	chr6:11762600-11763200	Weak transcription	Left Ventricle	heart
50	chr6:11762600-11763200	Weak transcription	NHDF-Ad	bronchial

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