Variant report

Variant	rs6678222
Chromosome Location	chr1:10158342-10158343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10158292-10158492	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
UBE4B	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11803995	1.00[GIH][hapmap]
rs11804755	1.00[EUR][1000 genomes]
rs17034549	1.00[EUR][1000 genomes]
rs17034554	1.00[ASW][hapmap];1.00[GIH][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs41280804	1.00[EUR][1000 genomes]
rs6679112	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6679221	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72859583	1.00[EUR][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	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10107400-10165400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:10109400-10158400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:10118200-10163000	Weak transcription	Aorta	Aorta
4	chr1:10120000-10162600	Weak transcription	Gastric	stomach
5	chr1:10120400-10163000	Weak transcription	Fetal Kidney	kidney
6	chr1:10125800-10165400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:10125800-10165400	Weak transcription	Fetal Brain Male	brain
8	chr1:10126000-10161000	Weak transcription	A549	lung
9	chr1:10126400-10162800	Weak transcription	Brain Germinal Matrix	brain
10	chr1:10126400-10163000	Weak transcription	Pancreas	Pancrea
11	chr1:10126400-10165400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:10132400-10163000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:10132600-10162600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:10132600-10165400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:10134600-10166200	Weak transcription	Colonic Mucosa	Colon
16	chr1:10134600-10166600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:10134800-10163000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:10135000-10160400	Weak transcription	Ovary	ovary
19	chr1:10135200-10164200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:10135200-10165400	Weak transcription	HUVEC	blood vessel
21	chr1:10135600-10162600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:10135800-10161200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:10135800-10164200	Weak transcription	NH-A	brain
24	chr1:10135800-10164200	Weak transcription	NHLF	lung
25	chr1:10136200-10164000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:10137600-10165600	Weak transcription	Esophagus	oesophagus
27	chr1:10137800-10161200	Weak transcription	Osteobl	bone
28	chr1:10140800-10162800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:10141000-10161000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:10141000-10164200	Weak transcription	Fetal Brain Female	brain
31	chr1:10141200-10158600	Weak transcription	Fetal Lung	lung
32	chr1:10142400-10161000	Weak transcription	Hela-S3	cervix
33	chr1:10143600-10161000	Weak transcription	NHDF-Ad	bronchial
34	chr1:10143800-10158400	Weak transcription	HSMM	muscle
35	chr1:10144000-10163000	Weak transcription	NHEK	skin
36	chr1:10144000-10165400	Weak transcription	HSMMtube	muscle
37	chr1:10144400-10159800	Weak transcription	GM12878-XiMat	blood
38	chr1:10144400-10163000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:10144400-10164000	Weak transcription	Right Ventricle	heart
40	chr1:10144600-10160800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:10145400-10162800	Weak transcription	HMEC	breast
42	chr1:10145400-10164200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:10145400-10189600	Weak transcription	Psoas Muscle	Psoas
44	chr1:10145600-10160400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:10145600-10162600	Weak transcription	HepG2	liver
46	chr1:10145600-10162800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:10145600-10163600	Weak transcription	Left Ventricle	heart
48	chr1:10145600-10164000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:10145600-10164400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:10145600-10165400	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links