Variant report

Variant	rs839838
Chromosome Location	chr1:77590565-77590566
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	chr1:77584058..77586581-chr1:77589256..77592005,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1098123	1.00[EUR][1000 genomes]
rs1098124	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1098127	1.00[EUR][1000 genomes]
rs11162308	1.00[CEU][hapmap]
rs1721152	1.00[AMR][1000 genomes]
rs1779182	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2177430	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2653470	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2799565	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2799569	1.00[EUR][1000 genomes]
rs55957022	0.81[AFR][1000 genomes]
rs58815389	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61484997	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74090599	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74090600	1.00[EUR][1000 genomes]
rs74092420	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839807	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs839812	1.00[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs839817	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs839819	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839820	0.82[AFR][1000 genomes]
rs839821	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs839833	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839837	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs839839	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77556000-77614400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:77568600-77595600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:77570800-77596800	Weak transcription	Left Ventricle	heart
4	chr1:77573400-77591200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:77574400-77613800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:77575000-77604000	Weak transcription	Primary B cells from cord blood	blood
7	chr1:77576800-77591400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:77578600-77607800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:77579800-77614200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:77581800-77599200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:77582400-77596400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:77583000-77598400	Weak transcription	Ovary	ovary
13	chr1:77585600-77619400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:77586400-77620600	Weak transcription	Primary T cells from cord blood	blood
15	chr1:77587000-77594600	Weak transcription	HSMM	muscle
16	chr1:77588000-77591400	Weak transcription	Fetal Brain Male	brain
17	chr1:77590400-77590600	Enhancers	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links