Variant report

Variant	rs979042
Chromosome Location	chr2:213146827-213146828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:213145552..213149044-chr2:213151103..213154081,3	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10048750	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs10048819	0.80[JPT][hapmap]
rs10164863	0.95[CEU][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10172782	0.83[CHB][hapmap]
rs10184205	0.83[CHD][hapmap]
rs1021916	0.86[CHB][hapmap]
rs1021917	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10932427	0.84[CHB][hapmap]
rs11682936	0.80[JPT][hapmap]
rs11887771	0.80[JPT][hapmap]
rs11896691	0.80[JPT][hapmap]
rs13408933	0.80[JPT][hapmap]
rs13429136	0.80[JPT][hapmap]
rs1357138	0.80[CHD][hapmap];0.80[JPT][hapmap]
rs1357139	0.86[CHD][hapmap]
rs1521639	0.80[JPT][hapmap]
rs1521641	0.80[JPT][hapmap]
rs1546718	0.80[JPT][hapmap]
rs1546719	0.80[JPT][hapmap]
rs1879651	0.85[CHB][hapmap]
rs1915747	0.85[CHB][hapmap]
rs1915748	0.93[CHB][hapmap]
rs1949654	0.81[JPT][hapmap]
rs2062932	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs4145960	0.86[CHD][hapmap]
rs4233985	0.80[CHD][hapmap];0.80[JPT][hapmap]
rs4375810	0.80[JPT][hapmap]
rs4580336	0.80[JPT][hapmap]
rs4638732	0.80[JPT][hapmap]
rs4672643	0.90[JPT][hapmap]
rs4673657	0.82[JPT][hapmap]
rs6717146	0.87[CHB][hapmap]
rs6727447	0.82[JPT][hapmap]
rs7561603	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs7570761	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs7570768	0.90[JPT][hapmap]
rs7577482	0.81[CHB][hapmap]
rs7580255	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs7583388	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs7608095	0.86[CHD][hapmap]
rs939224	0.80[CHD][hapmap];0.80[JPT][hapmap]
rs939226	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011572	chr2:212840066-213152279	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv875805	chr2:212891401-213164837	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875806	chr2:212997024-213211067	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1001718	chr2:213047033-213155985	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1004823	chr2:213052804-213181263	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv536138	chr2:213052804-213181263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1006051	chr2:213052804-213273642	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv584346	chr2:213067749-213258622	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv998615	chr2:213081893-213202228	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	nsv536139	chr2:213081893-213202228	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv460074	chr2:213114645-213151230	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	nsv584347	chr2:213114645-213151230	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv834526	chr2:213114901-213237146	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	nsv834527	chr2:213115966-213334308	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1011111	chr2:213116621-213178740	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
16	nsv460075	chr2:213117976-213192660	Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv584348	chr2:213117976-213192660	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
18	nsv584349	chr2:213117976-213200920	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	nsv460076	chr2:213120523-213165247	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	nsv584350	chr2:213120523-213165247	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
21	nsv875808	chr2:213120523-213183696	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
22	nsv460077	chr2:213122718-213165247	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
23	nsv584351	chr2:213122718-213165247	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
24	nsv875809	chr2:213122718-213221111	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
25	nsv460078	chr2:213130571-213192660	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
26	nsv584352	chr2:213130571-213192660	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
27	nsv584353	chr2:213136747-213191389	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
28	nsv875810	chr2:213136747-213200920	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
29	nsv460079	chr2:213136747-213209659	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
30	nsv584354	chr2:213136747-213209659	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
31	nsv584355	chr2:213136747-213211067	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
32	nsv1014680	chr2:213142147-213301614	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs979042	BARD1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213134400-213147400	Weak transcription	Brain Substantia Nigra	brain
2	chr2:213136600-213147400	Weak transcription	Psoas Muscle	Psoas
3	chr2:213141800-213147400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:213142000-213147200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:213146000-213149400	Enhancers	Fetal Heart	heart
6	chr2:213146200-213150200	Enhancers	Brain Hippocampus Middle	brain
7	chr2:213146800-213147200	Active TSS	Aorta	Aorta
8	chr2:213146800-213148400	Enhancers	Brain Cingulate Gyrus	brain
9	chr2:213146800-213149000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:213146800-213149600	Enhancers	Cortex derived primary cultured neurospheres	brain

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