Variant report

Variant	rs11257797
Chromosome Location	chr10:6322577-6322578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6319975..6324028-chr10:6337597..6341506,5	MCF-7	breast:
2	chr10:6319800..6323554-chr10:6441503..6444162,3	MCF-7	breast:
3	chr10:6320265..6323199-chr10:6333392..6336279,3	MCF-7	breast:
4	chr10:6320988..6323226-chr10:6428570..6430492,2	MCF-7	breast:
5	chr10:6243668..6247308-chr10:6319585..6323356,5	MCF-7	breast:
6	chr10:6288204..6291349-chr10:6321853..6323646,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10906080	1.00[YRI][hapmap]
rs11257741	1.00[YRI][hapmap]
rs17153464	1.00[CEU][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap]
rs56032229	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	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
6	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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6317800-6332600	Weak transcription	Thymus	Thymus
2	chr10:6318000-6337600	Weak transcription	Primary B cells from cord blood	blood
3	chr10:6318200-6323400	Weak transcription	Brain Substantia Nigra	brain
4	chr10:6318200-6333000	Weak transcription	Primary T cells from cord blood	blood
5	chr10:6318200-6333200	Weak transcription	Adipose Nuclei	Adipose
6	chr10:6318200-6337800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr10:6320600-6322600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr10:6320600-6322600	Enhancers	Fetal Intestine Large	intestine
9	chr10:6320600-6322800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr10:6320600-6322800	Enhancers	Fetal Intestine Small	intestine
11	chr10:6320600-6322800	Enhancers	HepG2	liver
12	chr10:6320800-6322600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr10:6320800-6322600	Enhancers	Stomach Mucosa	stomach
14	chr10:6320800-6322800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:6320800-6322800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:6320800-6322800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr10:6320800-6322800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr10:6321000-6322600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr10:6321000-6322800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:6321200-6322600	Enhancers	NHLF	lung
21	chr10:6321400-6322600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr10:6321400-6322600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:6321400-6322600	Enhancers	Fetal Kidney	kidney
24	chr10:6321400-6322600	Enhancers	HSMM	muscle
25	chr10:6321400-6322800	Enhancers	Pancreas	Pancrea
26	chr10:6321600-6322600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr10:6321800-6322600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:6321800-6322600	Enhancers	Brain Cingulate Gyrus	brain
29	chr10:6321800-6322600	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr10:6321800-6322800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:6321800-6322800	Flanking Active TSS	A549	lung
32	chr10:6321800-6323000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr10:6322000-6322600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr10:6322000-6322600	Enhancers	Liver	Liver
35	chr10:6322000-6322600	Enhancers	Brain Hippocampus Middle	brain
36	chr10:6322000-6322800	Enhancers	Primary T cells fromperipheralblood	blood
37	chr10:6322000-6323000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr10:6322200-6322600	Enhancers	Esophagus	oesophagus
39	chr10:6322200-6322600	Enhancers	Spleen	Spleen
40	chr10:6322200-6322800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr10:6322200-6322800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr10:6322200-6322800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr10:6322200-6322800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr10:6322200-6323600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr10:6322200-6328400	Weak transcription	Gastric	stomach
46	chr10:6322200-6330000	Weak transcription	Aorta	Aorta
47	chr10:6322400-6326400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links