Variant report

Variant	rs615546
Chromosome Location	chr10:6447061-6447062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6240172..6247565-chr10:6441706..6450964,34	MCF-7	breast:
2	chr10:6407311..6409448-chr10:6446152..6447736,2	MCF-7	breast:
3	chr10:6241662..6248347-chr10:6438932..6450669,77	MCF-7	breast:
4	chr10:6184712..6187301-chr10:6446699..6448973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10796089	1.00[EUR][1000 genomes]
rs11258372	1.00[EUR][1000 genomes]
rs11258441	1.00[EUR][1000 genomes]
rs11258935	1.00[EUR][1000 genomes]
rs11258970	1.00[EUR][1000 genomes]
rs34169455	1.00[EUR][1000 genomes]
rs584413	1.00[EUR][1000 genomes]
rs585932	1.00[EUR][1000 genomes]
rs586439	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs587378	1.00[EUR][1000 genomes]
rs599922	1.00[EUR][1000 genomes]
rs601150	1.00[EUR][1000 genomes]
rs601622	1.00[EUR][1000 genomes]
rs605806	1.00[EUR][1000 genomes]
rs611505	1.00[EUR][1000 genomes]
rs612497	1.00[EUR][1000 genomes]
rs617197	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs630027	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs631508	0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs644180	1.00[EUR][1000 genomes]
rs646830	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs647063	1.00[EUR][1000 genomes]
rs647279	1.00[EUR][1000 genomes]
rs650471	1.00[EUR][1000 genomes]
rs681023	1.00[EUR][1000 genomes]
rs682560	0.81[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7908102	1.00[EUR][1000 genomes]
rs806394	1.00[EUR][1000 genomes]
rs806395	1.00[EUR][1000 genomes]
rs806412	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6433800-6448600	Weak transcription	Primary T cells from cord blood	blood
2	chr10:6442000-6447200	Weak transcription	Spleen	Spleen
3	chr10:6443400-6452000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:6443800-6451800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr10:6444000-6447600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:6444000-6447600	Weak transcription	Pancreas	Pancrea
7	chr10:6444000-6447800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr10:6444000-6448200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr10:6444000-6448200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr10:6444000-6451200	Weak transcription	Aorta	Aorta
11	chr10:6444000-6451400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:6444000-6451600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:6444000-6452000	Weak transcription	Brain Anterior Caudate	brain
14	chr10:6444000-6452000	Weak transcription	Right Ventricle	heart
15	chr10:6444000-6452400	Weak transcription	Right Atrium	heart
16	chr10:6444200-6448000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:6444200-6448200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr10:6444200-6452000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr10:6444600-6447400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr10:6445200-6449000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr10:6445200-6451000	Weak transcription	Dnd41	blood
22	chr10:6445600-6450800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:6445600-6452000	Weak transcription	Psoas Muscle	Psoas
24	chr10:6445800-6448600	Weak transcription	Thymus	Thymus
25	chr10:6446000-6448600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr10:6446000-6452000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:6446400-6447800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links