Variant report

Variant	rs631817
Chromosome Location	chr1:85913740-85913741
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	chr1:85911377..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: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10489510	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10747318	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10782549	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873701	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1146374	0.84[AFR][1000 genomes]
rs1146383	0.88[EUR][1000 genomes]
rs12022248	0.88[ASN][1000 genomes]
rs12029221	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12032315	0.84[ASN][1000 genomes]
rs12033483	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12034249	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12035116	0.83[EUR][1000 genomes]
rs12038426	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12042780	0.81[EUR][1000 genomes]
rs12044882	0.81[ASN][1000 genomes]
rs12047189	0.81[EUR][1000 genomes]
rs1261681	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1342323	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1357635	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1357636	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1391556	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1523994	0.85[AFR][1000 genomes]
rs1523995	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1608537	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17384213	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17388696	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965876	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2016104	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2064510	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2124139	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2124140	0.88[ASN][1000 genomes]
rs2300633	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2389948	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851268	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4428939	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4512701	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4631749	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4949889	0.82[EUR][1000 genomes]
rs4949897	0.82[EUR][1000 genomes]
rs4949898	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4949899	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs499869	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs539714	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs561422	0.83[AFR][1000 genomes]
rs600098	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs604974	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6420965	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs659070	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6672870	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72722663	0.82[EUR][1000 genomes]
rs72722671	0.81[ASN][1000 genomes]
rs72722691	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72722692	0.83[AMR][1000 genomes]
rs72724608	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs731194	0.83[EUR][1000 genomes]
rs7515261	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7555670	0.80[EUR][1000 genomes]
rs990916	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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:67 , 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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links