Variant report

Variant	rs58648597
Chromosome Location	chr6:34359853-34359854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34203144..34206658-chr6:34358641..34361602,5	MCF-7	breast:
2	chr6:34359614..34360461-chr9:130742747..130743592,2	HCT-116	colon:
3	chr6:34359786..34360581-chrX:107334340..107334971,2	Hela-S3	cervix:
4	chr6:34336023..34338003-chr6:34357501..34359863,2	K562	blood:
5	chr6:34202422..34206409-chr6:34359682..34362061,4	MCF-7	breast:
6	chr19:34662845..34663493-chr6:34359460..34360357,2	Hela-S3	cervix:
7	chr6:34214133..34219385-chr6:34356600..34362053,16	K562	blood:
8	chr6:34202852..34208935-chr6:34358420..34361531,11	K562	blood:
9	chr6:34232571..34234778-chr6:34358274..34360439,2	K562	blood:
10	chr6:34242678..34244532-chr6:34357227..34359923,2	MCF-7	breast:
11	chr6:34202383..34217863-chr6:34357259..34364960,37	K562	blood:
12	chr6:34357967..34362826-chr6:34390808..34395314,8	K562	blood:
13	chr6:34213633..34219276-chr6:34358105..34363296,16	MCF-7	breast:
14	chr6:34358195..34361774-chr6:34391620..34393850,4	K562	blood:
15	chr6:34358377..34360251-chr6:34384641..34386602,2	MCF-7	breast:
16	chr6:34358853..34362255-chr6:34392162..34395391,9	MCF-7	breast:
17	chr6:34215295..34220270-chr6:34358417..34361933,11	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACSIN1-1	chr6:34355460-34360244	NONHSAT112133
2	lnc-PACSIN1-1	chr6:34359628-34362546	l_3174_chr6:34355416-34362546_76bGuttman_hLF

No data

Variant related genes	Relation type
ENSG00000186577	Chromatin interaction
ENSG00000167106	Chromatin interaction
ENSG00000270800	Chromatin interaction
ENSG00000137309	Chromatin interaction
ENSG00000101844	Chromatin interaction
ENSG00000101843	Chromatin interaction
ENSG00000257103	Chromatin interaction
ENSG00000124614	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12662460	0.93[ASN][1000 genomes]
rs12664001	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12664016	0.84[ASN][1000 genomes]
rs12665397	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16885998	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16889706	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16889714	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071928	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28847046	0.88[ASN][1000 genomes]
rs34384951	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3778077	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3798562	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3798564	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800476	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3800477	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4711390	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713770	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713772	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713773	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713774	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713775	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713776	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713777	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4713780	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713781	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713783	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713784	0.81[AMR][1000 genomes]
rs4713787	0.84[AMR][1000 genomes]
rs59310759	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60100381	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62399909	0.81[ASN][1000 genomes]
rs6924682	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6925243	0.87[ASN][1000 genomes]
rs6935129	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7752035	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7767431	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7775635	0.88[ASN][1000 genomes]
rs9766229	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1034978	chr6:34327526-34362187	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv981324	chr6:34351435-34360764	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34358000-34360800	Active TSS	HMEC	breast
2	chr6:34358000-34361000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:34358000-34361000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:34358000-34361200	Active TSS	NHLF	lung
5	chr6:34358200-34360800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:34358200-34361200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:34358200-34361400	Active TSS	Fetal Brain Female	brain
8	chr6:34358400-34360000	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr6:34358400-34360800	Active TSS	Fetal Intestine Small	intestine
10	chr6:34358400-34361000	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:34358400-34361000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:34358400-34361000	Active TSS	A549	lung
13	chr6:34358400-34361200	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr6:34358400-34361200	Active TSS	Aorta	Aorta
15	chr6:34358400-34361400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr6:34358400-34361600	Active TSS	Brain Hippocampus Middle	brain
17	chr6:34358600-34360000	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr6:34358600-34360000	Active TSS	Colonic Mucosa	Colon
19	chr6:34358600-34360800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:34358600-34360800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:34358600-34360800	Active TSS	Fetal Muscle Trunk	muscle
22	chr6:34358600-34360800	Active TSS	NHEK	skin
23	chr6:34358600-34361000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr6:34358600-34361000	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:34358600-34361000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:34358600-34361000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:34358600-34361000	Active TSS	Fetal Kidney	kidney
28	chr6:34358600-34361000	Active TSS	Stomach Mucosa	stomach
29	chr6:34358600-34361000	Active TSS	GM12878-XiMat	blood
30	chr6:34358600-34361000	Active TSS	HSMMtube	muscle
31	chr6:34358600-34361200	Active TSS	H1 Cell Line	embryonic stem cell
32	chr6:34358600-34361200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:34358600-34361200	Active TSS	Ovary	ovary
34	chr6:34358600-34361200	Active TSS	Psoas Muscle	Psoas
35	chr6:34358600-34361200	Active TSS	Right Ventricle	heart
36	chr6:34358600-34361200	Active TSS	HSMM	muscle
37	chr6:34358800-34360600	Active TSS	Stomach Smooth Muscle	stomach
38	chr6:34358800-34360800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr6:34358800-34360800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:34358800-34360800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:34358800-34360800	Active TSS	Muscle Satellite Cultured Cells	--
42	chr6:34358800-34360800	Active TSS	Fetal Heart	heart
43	chr6:34358800-34360800	Active TSS	Hela-S3	cervix
44	chr6:34358800-34361000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:34358800-34361000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:34358800-34361000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:34358800-34361000	Active TSS	Colon Smooth Muscle	Colon
48	chr6:34358800-34361000	Active TSS	NHDF-Ad	bronchial
49	chr6:34358800-34361200	Active TSS	H9 Cell Line	embryonic stem cell
50	chr6:34358800-34361200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links