Variant report

Variant	rs3095151
Chromosome Location	chr6:30900150-30900151
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30900149-30900199	SAEC	small airway:	n/a
2	chr6:30900149-30900199	NHDF-neo	bronchial:	n/a
3	chr6:30900149-30900199	SK-N-SH_RA	brain:	n/a
4	chr6:30900149-30900199	ECC-1	luminal epithelium:	n/a
5	chr6:30900149-30900199	HRPEpiC	eye:	n/a
6	chr6:30900149-30900199	NB4	blood:	n/a
7	chr6:30900149-30900199	HAEpiC	amniotic membrane:	n/a
8	chr6:30900149-30900199	Caco-2	colon:	n/a
9	chr6:30900149-30900199	HRE	kidney:	n/a
10	chr6:30900149-30900199	HIPEpiC	eye:	n/a
11	chr6:30900149-30900199	BE2_C	brain:	n/a
12	chr6:30900149-30900199	HEK293	kidney:	embryo
13	chr6:30900149-30900199	LNCaP	prostate:	n/a
14	chr6:30900149-30900199	IMR90	lung:	fetal
15	chr6:30900149-30900199	GM12878	blood:	n/a
16	chr6:30900149-30900199	HCM	heart:	n/a
17	chr6:30900149-30900199	ovcar-3	ovarian:	n/a
18	chr6:30900149-30900199	AoSMC	blood vessel:	n/a
19	chr6:30900149-30900199	GM06990	blood:	n/a
20	chr6:30900149-30900199	Hepatocyte	liver:	n/a
21	chr6:30900149-30900199	GM19239	blood:	n/a
22	chr6:30900149-30900199	SK-N-SH	brain:	n/a
23	chr6:30900149-30900199	NHBE	bronchial:	n/a
24	chr6:30900149-30900199	HPAEpiC	pulmonary alveolar:	n/a
25	chr6:30900149-30900199	HRCEpiC	kidney:	n/a
26	chr6:30900149-30900199	T-47D	breast:	n/a
27	chr6:30900149-30900199	Jurkat	blood:	n/a
28	chr6:30900149-30900199	HCF	heart:	n/a
29	chr6:30900149-30900199	H1-hESC	embryonic stem cell:	embryo
30	chr6:30900149-30900199	AG04450	lung:	fetal
31	chr6:30900149-30900199	HUVEC	blood vessel:	n/a
32	chr6:30900149-30900199	HepG2	liver:	n/a
33	chr6:30900149-30900199	HCT-116	colon:	n/a
34	chr6:30900149-30900199	PFSK-1	brain:	n/a
35	chr6:30900149-30900199	AG04449	skin:	fetal
36	chr6:30900149-30900199	Hela-S3	cervix:	n/a
37	chr6:30900149-30900199	GM12891	blood:	n/a
38	chr6:30900149-30900199	PrEC	prostate:	n/a
39	chr6:30900149-30900199	AG09309	skin:	n/a
40	chr6:30900149-30900199	AG10803	skin:	n/a
41	chr6:30900149-30900199	HCPEpiC	choroid plexus:	n/a
42	chr6:30900149-30900199	SK-N-MC	brain:	n/a
43	chr6:30900149-30900199	MCF10A-Er-Src	breast:	n/a
44	chr6:30900149-30900199	ProgFib	skin:	n/a
45	chr6:30900149-30900199	NH-A	brain:	n/a
46	chr6:30900149-30900199	HL-60	blood:	n/a
47	chr6:30900149-30900199	HMEC	breast:	n/a
48	chr6:30900149-30900199	CMK	blood:	n/a
49	chr6:30900149-30900199	PANC-1	pancreas:	n/a
50	chr6:30900149-30900199	GM12892	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30899631..30901775-chr6:30921844..30924494,3	K562	blood:

No data

Variant related genes	Relation type
SFTA2	CpG island
ENSG00000233529	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs3095152	0.85[ASN][1000 genomes]
rs3095153	0.85[ASN][1000 genomes]
rs3095154	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130781	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3131787	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3095151	VARS2	cis	lymphoblastoid	seeQTL
rs3095151	HIST1H2AM	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30894800-30901000	Weak transcription	Fetal Kidney	kidney
2	chr6:30894800-30902600	Weak transcription	NHEK	skin
3	chr6:30894800-30903000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:30894800-30905000	Weak transcription	Right Ventricle	heart
5	chr6:30896000-30904400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:30896600-30905800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:30897000-30900200	Weak transcription	A549	lung
8	chr6:30897000-30904000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:30897000-30905600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:30897000-30905800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:30897000-30909800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:30897200-30905600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:30897400-30903000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:30898200-30902200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:30899200-30900200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:30899200-30903400	Enhancers	Fetal Intestine Large	intestine
17	chr6:30899200-30904200	Enhancers	Fetal Intestine Small	intestine
18	chr6:30899400-30900200	Flanking Active TSS	Stomach Mucosa	stomach
19	chr6:30899400-30900400	Weak transcription	Fetal Lung	lung
20	chr6:30899400-30900800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:30899400-30904600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:30899600-30900200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:30899600-30900800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:30899800-30900200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:30899800-30900200	Enhancers	HMEC	breast
26	chr6:30899800-30901000	Enhancers	Duodenum Mucosa	Duodenum
27	chr6:30899800-30901200	Enhancers	Gastric	stomach
28	chr6:30900000-30900400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr6:30900000-30900600	Weak transcription	Lung	lung
30	chr6:30900000-30900800	Enhancers	Small Intestine	intestine
31	chr6:30900000-30901000	Enhancers	Esophagus	oesophagus
32	chr6:30900000-30902000	Enhancers	Pancreas	Pancrea

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