Variant report

Variant	rs11161617
Chromosome Location	chr1:85913538-85913539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85913232..85915386-chr1:85917552..85919124,2	K562	blood:
2	chr1:85912844..85915674-chr1:86040925..86042753,2	MCF-7	breast:
3	chr1:85863358..85866240-chr1:85910699..85913658,2	K562	blood:
4	chr1:85911377..85913833-chr1:85913866..85915628,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYR61-3	chr1:85913481-85913807	ENSG00000223653

Variant related genes	Relation type
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10782550	0.82[EUR][1000 genomes]
rs11161599	0.80[CEU][hapmap]
rs11161614	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161615	0.90[CEU][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes]
rs11161616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11801146	0.84[AFR][1000 genomes]
rs12049529	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12129013	0.82[CEU][hapmap]
rs12130145	0.80[CEU][hapmap]
rs12130380	0.90[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12130591	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12131926	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12138852	0.86[JPT][hapmap]
rs12717763	0.80[CEU][hapmap]
rs12724823	0.85[CEU][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs1498374	0.80[CEU][hapmap]
rs2076699	0.80[CEU][hapmap]
rs2300639	0.80[CEU][hapmap]
rs28529751	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35761966	0.88[EUR][1000 genomes]
rs986639	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv441699	chr1:85911291-85915402	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85886400-85914200	Weak transcription	HSMMtube	muscle
2	chr1:85893800-85916800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:85899200-85914800	Weak transcription	Esophagus	oesophagus
4	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:85904400-85914800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:85905200-85914800	Weak transcription	Small Intestine	intestine
7	chr1:85906800-85914200	Weak transcription	Ovary	ovary
8	chr1:85907000-85914200	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:85907000-85914600	Weak transcription	Fetal Stomach	stomach
10	chr1:85907000-85914800	Weak transcription	Aorta	Aorta
11	chr1:85907000-85914800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:85907000-85919600	Weak transcription	Right Atrium	heart
13	chr1:85909200-85916600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:85910400-85916000	Weak transcription	HMEC	breast
15	chr1:85910600-85914800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:85911200-85914000	Weak transcription	Stomach Mucosa	stomach
17	chr1:85911200-85917200	Enhancers	NHDF-Ad	bronchial
18	chr1:85911400-85914800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:85911400-85915000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:85911800-85916600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:85912000-85914400	Enhancers	H9 Cell Line	embryonic stem cell
22	chr1:85912000-85914400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:85912000-85914600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:85912200-85913800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr1:85912200-85913800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr1:85912200-85913800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:85912200-85914000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr1:85912200-85914000	Enhancers	HUVEC	blood vessel
29	chr1:85912200-85914200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:85912200-85914200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:85912200-85914400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:85912200-85914800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:85912200-85914800	Enhancers	NHLF	lung
34	chr1:85912200-85915600	Genic enhancers	HSMM	muscle
35	chr1:85912200-85916000	Enhancers	Liver	Liver
36	chr1:85912200-85917400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:85912400-85914800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:85912400-85915400	Enhancers	Brain Anterior Caudate	brain
39	chr1:85912600-85913800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:85912800-85913800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:85912800-85913800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:85912800-85913800	Enhancers	Adipose Nuclei	Adipose
43	chr1:85912800-85913800	Enhancers	Fetal Intestine Large	intestine
44	chr1:85912800-85913800	Enhancers	Fetal Intestine Small	intestine
45	chr1:85912800-85913800	Enhancers	Left Ventricle	heart
46	chr1:85912800-85913800	Enhancers	Psoas Muscle	Psoas
47	chr1:85912800-85914800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:85912800-85915000	Enhancers	NH-A	brain
49	chr1:85912800-85915800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr1:85912800-85916000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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