Variant report

Variant	rs666103
Chromosome Location	chr1:10511589-10511590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10508493..10514342-chr1:10516490..10519388,5	K562	blood:
2	chr1:10507112..10511032-chr1:10511336..10515640,6	K562	blood:
3	chr1:10498763..10502281-chr1:10507283..10512164,5	K562	blood:

Variant related genes	Relation type
ENSG00000241563	Chromatin interaction
ENSG00000175279	Chromatin interaction
ENSG00000203469	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10864455	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1188530	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1307489	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1307490	1.00[CEU][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1307493	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1307494	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1307497	0.82[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1308520	1.00[CEU][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2480782	1.00[TSI][hapmap]
rs2483686	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2847336	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2847337	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs484416	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs490037	0.84[EUR][1000 genomes]
rs490960	0.84[EUR][1000 genomes]
rs515423	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs544289	0.82[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs647281	0.82[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6540931	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs661256	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs661272	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs676995	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7537164	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs944973	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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 target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10491400-10519000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:10491400-10521000	Weak transcription	Ovary	ovary
3	chr1:10491400-10521200	Weak transcription	Aorta	Aorta
4	chr1:10491600-10516200	Weak transcription	HMEC	breast
5	chr1:10491600-10517800	Weak transcription	Primary T cells from cord blood	blood
6	chr1:10491600-10518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:10491600-10518000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:10491600-10519200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:10491600-10521200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:10491600-10521200	Weak transcription	Left Ventricle	heart
11	chr1:10491600-10521200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:10491600-10521200	Weak transcription	Spleen	Spleen
13	chr1:10491600-10521400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:10491800-10516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:10491800-10516600	Weak transcription	HSMM	muscle
16	chr1:10491800-10520600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:10492000-10521200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:10492400-10517200	Weak transcription	Brain Germinal Matrix	brain
19	chr1:10493600-10516800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:10494200-10518800	Weak transcription	K562	blood
21	chr1:10494200-10521400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:10495400-10519000	Weak transcription	Placenta	Placenta
23	chr1:10499200-10531400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:10499400-10519200	Weak transcription	HepG2	liver
25	chr1:10499600-10518200	Weak transcription	Primary B cells from cord blood	blood
26	chr1:10500800-10522800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:10501200-10516200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:10501200-10519200	Weak transcription	Liver	Liver
29	chr1:10501200-10521400	Weak transcription	Brain Angular Gyrus	brain
30	chr1:10503000-10511600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:10503400-10518000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:10503800-10518200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:10505200-10519200	Weak transcription	Hela-S3	cervix
34	chr1:10505200-10520600	Weak transcription	Lung	lung
35	chr1:10505400-10514600	Weak transcription	Fetal Thymus	thymus
36	chr1:10505400-10518000	Weak transcription	Dnd41	blood
37	chr1:10506000-10514600	Weak transcription	Thymus	Thymus
38	chr1:10507000-10514400	Weak transcription	Fetal Intestine Large	intestine
39	chr1:10507400-10517000	Weak transcription	A549	lung
40	chr1:10508600-10516000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:10508800-10521200	Weak transcription	Pancreas	Pancrea
42	chr1:10509400-10511800	Enhancers	Fetal Muscle Leg	muscle
43	chr1:10509400-10512400	Enhancers	Fetal Brain Male	brain
44	chr1:10509600-10512000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr1:10509600-10514600	Weak transcription	Fetal Intestine Small	intestine
46	chr1:10509800-10521400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:10510000-10512000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:10510000-10512400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr1:10510200-10511800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:10510400-10512000	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links