Variant report

Variant	rs6587945
Chromosome Location	chr1:62176781-62176782
allele	A/G
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	FOSL2	chr1:62176779-62177246	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62173080..62176930-chr1:62205875..62209587,4	MCF-7	breast:
2	chr1:62173473..62177807-chr1:62188633..62191997,6	K562	blood:

Variant related genes	Relation type
TM2D1	TF binding region
ENSG00000132849	Chromatin interaction
ENSG00000162604	Chromatin interaction
ENSG00000271200	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1151760	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1151763	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1151765	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1151774	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11578760	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12753030	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12754462	0.94[EUR][1000 genomes]
rs1286623	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286635	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1286636	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1286639	0.87[ASN][1000 genomes]
rs1315521	0.80[ASN][1000 genomes]
rs1390450	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1692130	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787461	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61770089	0.80[ASN][1000 genomes]
rs6686930	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
2	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
2	chr1:62140000-62189000	Weak transcription	NHLF	lung
3	chr1:62142800-62188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:62146200-62190200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:62158600-62189800	Weak transcription	Pancreas	Pancrea
6	chr1:62161200-62180600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:62161800-62179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:62162600-62177400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:62163400-62181800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:62165000-62189800	Weak transcription	Aorta	Aorta
11	chr1:62165400-62189400	Weak transcription	Fetal Brain Male	brain
12	chr1:62165400-62189600	Weak transcription	Right Ventricle	heart
13	chr1:62165400-62189800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:62166400-62189400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:62166600-62187400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:62166600-62189400	Weak transcription	A549	lung
17	chr1:62166800-62178000	Weak transcription	Brain Angular Gyrus	brain
18	chr1:62166800-62189400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:62167600-62177200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:62168400-62177600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:62169600-62177400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:62169600-62179400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:62169600-62179600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:62169600-62181200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:62170000-62179200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:62171600-62188400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:62172000-62189400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:62172000-62189800	Weak transcription	Gastric	stomach
29	chr1:62173000-62184000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:62173200-62189600	Weak transcription	Colonic Mucosa	Colon
31	chr1:62174000-62189600	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:62174200-62189000	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:62174400-62188800	Weak transcription	Brain Germinal Matrix	brain
34	chr1:62174400-62189800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:62174400-62189800	Weak transcription	Esophagus	oesophagus
36	chr1:62174600-62177000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:62174600-62184800	Weak transcription	HUVEC	blood vessel
38	chr1:62174600-62189200	Weak transcription	HepG2	liver
39	chr1:62174600-62190200	Weak transcription	Small Intestine	intestine
40	chr1:62174800-62176800	Weak transcription	Thymus	Thymus
41	chr1:62174800-62177000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:62174800-62177200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:62174800-62178400	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:62174800-62180000	Weak transcription	Fetal Intestine Small	intestine
45	chr1:62174800-62182600	Weak transcription	NHEK	skin
46	chr1:62174800-62189200	Weak transcription	Fetal Brain Female	brain
47	chr1:62174800-62189400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:62174800-62189600	Weak transcription	Primary B cells from cord blood	blood
49	chr1:62174800-62189600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:62174800-62189600	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links