Variant report

Variant	rs4951539
Chromosome Location	chr1:211805885-211805886
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:211802788..211806999-chr1:211814684..211819078,4	K562	blood:
2	chr1:211804616..211806935-chr1:211847772..211850584,2	K562	blood:
3	chr1:211805499..211810389-chr1:211816053..211819078,4	K562	blood:
4	chr1:211782443..211790536-chr1:211800686..211806134,8	K562	blood:
5	chr1:211751888..211754442-chr1:211802354..211807016,4	K562	blood:
6	chr1:211750004..211752900-chr1:211803932..211806097,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117650	Chromatin interaction
ENSG00000170385	Chromatin interaction
ENSG00000228792	Chromatin interaction
ENSG00000231057	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10158305	0.82[EUR][1000 genomes]
rs10158307	0.82[EUR][1000 genomes]
rs10158309	0.82[EUR][1000 genomes]
rs10158749	0.83[EUR][1000 genomes]
rs10158790	0.82[EUR][1000 genomes]
rs10158874	0.83[EUR][1000 genomes]
rs10159253	0.82[EUR][1000 genomes]
rs10779564	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779565	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863920	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119787	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11576789	0.80[CEU][hapmap]
rs12087826	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs12090722	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12123429	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12142250	0.82[EUR][1000 genomes]
rs12727505	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12741252	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12758005	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs1373293	0.82[EUR][1000 genomes]
rs35531215	0.80[EUR][1000 genomes]
rs4245741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951415	0.92[ASN][1000 genomes]
rs4951416	0.91[CEU][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951418	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951421	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951537	0.85[ASN][1000 genomes]
rs4951540	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61851777	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540697	0.81[AMR][1000 genomes]
rs6540698	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6660850	0.81[AMR][1000 genomes]
rs6669878	0.82[EUR][1000 genomes]
rs6670986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6671497	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6671506	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675796	0.84[CEU][hapmap]
rs6682640	0.85[AMR][1000 genomes]
rs7513348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7523748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527270	1.00[CHB][hapmap]
rs894853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs894854	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs894855	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211800000-211807200	Enhancers	Fetal Heart	heart
2	chr1:211802000-211806400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:211803400-211806000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:211803400-211807000	Enhancers	Ovary	ovary
5	chr1:211803400-211807600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:211803400-211807600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:211803600-211807200	Enhancers	Fetal Muscle Trunk	muscle
8	chr1:211803600-211807200	Enhancers	Fetal Muscle Leg	muscle
9	chr1:211803800-211807600	Enhancers	Fetal Thymus	thymus
10	chr1:211804000-211806400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:211804000-211806400	Weak transcription	Gastric	stomach
12	chr1:211804000-211806800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:211804200-211806400	Weak transcription	A549	lung
14	chr1:211804200-211807200	Enhancers	Right Atrium	heart
15	chr1:211804200-211807200	Enhancers	Right Ventricle	heart
16	chr1:211804200-211807600	Enhancers	Left Ventricle	heart
17	chr1:211804200-211813400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:211804200-211816600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:211804400-211806200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:211804400-211806200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:211804400-211806400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:211804400-211807400	Enhancers	Spleen	Spleen
23	chr1:211804400-211809400	Enhancers	Hela-S3	cervix
24	chr1:211804800-211806000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:211804800-211806000	Weak transcription	Adipose Nuclei	Adipose
26	chr1:211804800-211806200	Weak transcription	Fetal Intestine Small	intestine
27	chr1:211804800-211806400	Weak transcription	Fetal Intestine Large	intestine
28	chr1:211804800-211806400	Enhancers	HepG2	liver
29	chr1:211804800-211806400	Enhancers	K562	blood
30	chr1:211805000-211807000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:211805200-211806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:211805400-211806800	Enhancers	GM12878-XiMat	blood
33	chr1:211805400-211807000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:211805400-211807000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:211805400-211807000	Enhancers	Colon Smooth Muscle	Colon
36	chr1:211805400-211807400	Enhancers	Osteobl	bone
37	chr1:211805400-211808200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:211805400-211808200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:211805600-211806600	Enhancers	Brain Anterior Caudate	brain
40	chr1:211805600-211807000	Enhancers	Esophagus	oesophagus
41	chr1:211805600-211807000	Enhancers	Fetal Lung	lung
42	chr1:211805600-211807200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:211805600-211807200	Enhancers	HSMM	muscle
44	chr1:211805600-211807400	Enhancers	NH-A	brain
45	chr1:211805600-211807800	Enhancers	HMEC	breast
46	chr1:211805800-211806000	Enhancers	Primary hematopoietic stem cells	blood
47	chr1:211805800-211806800	Bivalent Enhancer	Fetal Stomach	stomach
48	chr1:211805800-211807000	Enhancers	Placenta	Placenta
49	chr1:211805800-211807000	Enhancers	Lung	lung
50	chr1:211805800-211807000	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links