Variant report

Variant	rs6900929
Chromosome Location	chr6:53716382-53716383
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	chr6:53714815..53716814-chr6:53717074..53718725,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13197492	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3000998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3001003	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3003496	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3003497	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4077760	0.86[CHB][hapmap]
rs4269375	0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4276503	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4276504	0.82[CHB][hapmap]
rs4342426	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4357137	0.82[CHB][hapmap]
rs4475321	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4476827	0.85[CHB][hapmap]
rs4587161	0.87[EUR][1000 genomes]
rs4715425	0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5001609	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6458960	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6905927	0.86[CHB][hapmap]
rs6934444	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7767443	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9349686	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9357774	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9357775	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9367542	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9370236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382239	0.92[AMR][1000 genomes];0.95[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
3	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:53703000-53718600	Weak transcription	Pancreas	Pancrea
7	chr6:53703200-53720000	Weak transcription	HSMMtube	muscle
8	chr6:53703200-53720200	Weak transcription	Aorta	Aorta
9	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
10	chr6:53703800-53717200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:53705400-53718800	Weak transcription	NHEK	skin
13	chr6:53706000-53720200	Weak transcription	Esophagus	oesophagus
14	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:53706400-53720200	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:53707600-53718800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:53707800-53718800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:53709400-53718600	Weak transcription	Gastric	stomach
20	chr6:53709600-53719800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:53709800-53719800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
23	chr6:53710400-53720400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:53711200-53718800	Weak transcription	Fetal Intestine Large	intestine
25	chr6:53711200-53719800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:53711200-53720400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:53711400-53719600	Weak transcription	Thymus	Thymus
28	chr6:53712600-53720400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:53712800-53719600	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:53712800-53720000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:53712800-53721600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:53713000-53717200	Weak transcription	Brain Substantia Nigra	brain
33	chr6:53713000-53719000	Weak transcription	Primary T cells from cord blood	blood
34	chr6:53713000-53719800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:53713000-53719800	Weak transcription	Fetal Thymus	thymus
36	chr6:53713000-53720000	Weak transcription	Brain Anterior Caudate	brain
37	chr6:53713000-53720200	Weak transcription	Dnd41	blood
38	chr6:53713000-53722000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:53713200-53719800	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:53713200-53720000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:53713400-53718400	Weak transcription	HepG2	liver
42	chr6:53715600-53716400	Enhancers	Brain Angular Gyrus	brain
43	chr6:53716200-53716400	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links