Variant report

Variant	rs10494751
Chromosome Location	chr1:197168625-197168626
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr1:197168577-197168724	K562	blood:	n/a	n/a
2	POLR2A	chr1:197168622-197168646	MCF-7	breast:	n/a	n/a
3	ARID3A	chr1:197168611-197169006	K562	blood:	n/a	n/a
4	POLR2A	chr1:197168598-197168720	GM12878	blood:	n/a	n/a
5	HCFC1	chr1:197168459-197172025	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:197152680..197155309-chr1:197165847..197169413,3	MCF-7	breast:
2	chr1:197153884..197156331-chr1:197167263..197169035,2	K562	blood:
3	chr1:197112577..197117711-chr1:197168565..197172597,7	K562	blood:

Variant related genes	Relation type
CRB1	TF binding region
ENSG00000066279	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10494748	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10494749	0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10494750	0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11800461	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11801772	0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11803081	1.00[AMR][1000 genomes]
rs11808524	0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11808883	0.81[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11809963	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11810041	0.85[AMR][1000 genomes]
rs11811295	0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11811814	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1337165	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841212	0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841214	0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841219	0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841220	0.88[ASW][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841237	0.82[ASW][hapmap];0.88[LWK][hapmap];0.82[MKK][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841270	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59820773	1.00[ASN][1000 genomes]
rs61170532	1.00[AMR][1000 genomes]
rs61172533	1.00[ASN][1000 genomes]
rs6700604	1.00[ASN][1000 genomes]
rs6702338	1.00[ASN][1000 genomes]
rs6702739	1.00[ASN][1000 genomes]
rs7535048	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:197125600-197169600	Weak transcription	Esophagus	oesophagus
3	chr1:197126400-197169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:197157400-197169400	Weak transcription	Colonic Mucosa	Colon
5	chr1:197157400-197169600	Weak transcription	Pancreas	Pancrea
6	chr1:197159400-197169600	Weak transcription	Gastric	stomach
7	chr1:197159400-197169800	Weak transcription	Lung	lung
8	chr1:197159600-197169200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:197159600-197169800	Weak transcription	Spleen	Spleen
10	chr1:197159800-197169600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:197160600-197169200	Weak transcription	Fetal Stomach	stomach
12	chr1:197161000-197169200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:197161000-197169400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:197161000-197169400	Weak transcription	Placenta	Placenta
15	chr1:197161600-197168800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:197163400-197169400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:197163600-197168800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:197164000-197168800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr1:197164000-197169200	Active TSS	GM12878-XiMat	blood
20	chr1:197164800-197169400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:197165000-197169400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:197165600-197169200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:197166200-197170000	Flanking Active TSS	Dnd41	blood
24	chr1:197166400-197171400	Active TSS	K562	blood
25	chr1:197166400-197171600	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:197166400-197171600	Active TSS	Right Atrium	heart
27	chr1:197166600-197171600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:197166800-197168800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:197166800-197169200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:197166800-197169800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:197166800-197171400	Active TSS	HSMMtube	muscle
32	chr1:197166800-197171600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:197166800-197171800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:197167000-197168800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr1:197167000-197169600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:197167200-197168800	Active TSS	NH-A	brain
37	chr1:197167200-197169000	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr1:197167200-197169600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:197167200-197169600	Weak transcription	Small Intestine	intestine
40	chr1:197167200-197171600	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:197167200-197171600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:197167200-197171600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:197167200-197171600	Active TSS	Fetal Intestine Large	intestine
44	chr1:197167400-197169000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:197167400-197169200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:197167400-197169200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:197167400-197169400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr1:197167400-197169400	Active TSS	Brain Germinal Matrix	brain
49	chr1:197167400-197169600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:197167400-197169800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links