Variant report

Variant	rs10906429
Chromosome Location	chr10:6440676-6440677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6268377..6270952-chr10:6439615..6442494,2	MCF-7	breast:
2	chr10:6433732..6435760-chr10:6438593..6441189,2	MCF-7	breast:
3	chr10:6335347..6345426-chr10:6438966..6446500,25	MCF-7	breast:
4	chr10:6405295..6407901-chr10:6440170..6443280,3	MCF-7	breast:
5	chr10:6355714..6359747-chr10:6439655..6444608,4	MCF-7	breast:
6	chr10:6242682..6246426-chr10:6435409..6441608,6	MCF-7	breast:
7	chr10:6241662..6248347-chr10:6438932..6450669,77	MCF-7	breast:
8	chr10:6213842..6217578-chr10:6440215..6444300,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction
ENSG00000226705	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11258500	0.86[ASW][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11258501	0.84[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11258515	0.89[AFR][1000 genomes]
rs12413588	1.00[CHB][hapmap]
rs12572911	0.86[ASW][hapmap];1.00[YRI][hapmap]
rs2296125	0.86[ASW][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2296126	1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[ASN][1000 genomes]
rs681604	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs7916702	1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[ASN][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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6425600-6443600	Weak transcription	Aorta	Aorta
2	chr10:6433800-6448600	Weak transcription	Primary T cells from cord blood	blood
3	chr10:6434600-6443600	Weak transcription	Fetal Brain Female	brain
4	chr10:6436400-6441400	Weak transcription	Fetal Lung	lung
5	chr10:6436400-6443600	Weak transcription	Fetal Kidney	kidney
6	chr10:6436600-6443400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:6436600-6443400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr10:6437200-6444000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr10:6437600-6444400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr10:6438600-6441000	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr10:6438600-6441600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:6439000-6441000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:6439200-6441000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:6439200-6443400	Weak transcription	NHEK	skin
15	chr10:6439400-6440800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:6439600-6441000	Enhancers	A549	lung
17	chr10:6439600-6441000	Weak transcription	HMEC	breast
18	chr10:6440000-6440800	Weak transcription	Primary B cells from cord blood	blood
19	chr10:6440200-6441400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr10:6440400-6441200	Enhancers	Brain Cingulate Gyrus	brain
21	chr10:6440400-6441200	Enhancers	NHDF-Ad	bronchial
22	chr10:6440400-6442000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr10:6440400-6443400	Enhancers	Brain Substantia Nigra	brain
24	chr10:6440400-6443600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:6440600-6440800	Enhancers	Brain Germinal Matrix	brain
26	chr10:6440600-6441400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr10:6440600-6442000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:6440600-6442200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr10:6440600-6443600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr10:6440600-6444000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links