Variant report

Variant	rs946226
Chromosome Location	chr6:45898193-45898194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45897955..45898801-chr6:46057521..46058514,3	MCF-7	breast:
2	chr6:45897904..45898920-chr6:46377652..46378792,5	K562	blood:
3	chr6:45897935..45898821-chr6:46377732..46378655,2	MCF-7	breast:
4	chr6:45897865..45898727-chr6:45982870..45983433,2	MCF-7	breast:
5	chr6:45896173..45899025-chr6:45900583..45902149,3	K562	blood:

Variant related genes	Relation type
ENSG00000112782	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12055836	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12662995	0.89[AMR][1000 genomes]
rs3777566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777569	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777574	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3777575	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3777578	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs3798263	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798266	1.00[CEU][hapmap]
rs3822886	0.89[AMR][1000 genomes]
rs6907979	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs9357496	0.89[AMR][1000 genomes]
rs9395137	0.84[AMR][1000 genomes]
rs949678	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[AMR][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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1021917	chr6:45879064-45898314	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45866600-45898400	Weak transcription	Colonic Mucosa	Colon
2	chr6:45881200-45908000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:45882400-45898400	Weak transcription	Fetal Intestine Large	intestine
4	chr6:45886800-45910600	Weak transcription	Psoas Muscle	Psoas
5	chr6:45890600-45901600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:45891000-45898400	Weak transcription	Fetal Kidney	kidney
7	chr6:45891600-45898400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:45894400-45898600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:45894800-45898400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:45895400-45910800	Weak transcription	Placenta	Placenta
11	chr6:45895600-45898800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:45896200-45898200	Weak transcription	Fetal Stomach	stomach
13	chr6:45896200-45901400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:45896400-45899200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:45896600-45898400	Strong transcription	Fetal Intestine Small	intestine
16	chr6:45896600-45898400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr6:45897200-45898400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:45897200-45899200	Enhancers	Fetal Lung	lung
19	chr6:45897400-45898600	Enhancers	Left Ventricle	heart
20	chr6:45897400-45899200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:45897400-45899200	Enhancers	Right Ventricle	heart
22	chr6:45897400-45899400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr6:45897600-45898400	Weak transcription	Osteobl	bone
24	chr6:45897800-45898200	Enhancers	Fetal Muscle Trunk	muscle
25	chr6:45897800-45898600	Enhancers	Brain Germinal Matrix	brain
26	chr6:45897800-45898600	Enhancers	Stomach Smooth Muscle	stomach
27	chr6:45897800-45898800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr6:45897800-45901400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:45898000-45898200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr6:45898000-45898200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr6:45898000-45898200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:45898000-45898600	Enhancers	Right Atrium	heart
33	chr6:45898000-45898600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr6:45898000-45898800	Enhancers	H9 Cell Line	embryonic stem cell
35	chr6:45898000-45898800	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr6:45898000-45898800	Enhancers	Brain Substantia Nigra	brain
37	chr6:45898000-45899000	Enhancers	Fetal Heart	heart
38	chr6:45898000-45899200	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links