Variant report

Variant	rs870339
Chromosome Location	chr3:195962244-195962245
allele	G/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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195951172..195953853-chr3:195961938..195964763,2	K562	blood:
2	chr3:195868576..195870552-chr3:195961996..195964439,2	MCF-7	breast:
3	chr3:195960645..195963249-chr3:195964998..195967622,2	MCF-7	breast:
4	chr3:195961871..195966167-chr3:195972048..195974427,4	K562	blood:
5	chr3:195957001..195958662-chr3:195962028..195964022,2	MCF-7	breast:
6	chr3:195961871..195964800-chr3:195972048..195973919,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCTEX1D2-3	chr3:195961240-195964785	NONHSAT094312

No data

Variant related genes	Relation type
ENSG00000224652	Chromatin interaction
ENSG00000163959	Chromatin interaction
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11185519	0.95[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12491227	0.85[JPT][hapmap]
rs12629949	0.80[ASN][1000 genomes]
rs12632779	0.83[MEX][hapmap]
rs12637288	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1476331	0.85[JPT][hapmap]
rs1476332	0.92[JPT][hapmap]
rs1875088	0.95[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1948690	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2047550	0.82[CHB][hapmap]
rs2047551	0.94[CHB][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2088666	0.94[CHB][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs2342309	0.81[JPT][hapmap]
rs3772109	0.88[CHB][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs4396926	0.81[ASN][1000 genomes]
rs4916421	0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4916456	0.81[ASN][1000 genomes]
rs4916485	0.82[CHB][hapmap]
rs56867360	0.85[EUR][1000 genomes]
rs56875789	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58297632	0.81[ASN][1000 genomes]
rs59289255	0.81[ASN][1000 genomes]
rs59352354	0.81[ASN][1000 genomes]
rs60276076	0.83[EUR][1000 genomes]
rs61608982	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66487782	0.81[ASN][1000 genomes]
rs66780758	0.81[ASN][1000 genomes]
rs66805306	0.81[ASN][1000 genomes]
rs66927787	0.81[ASN][1000 genomes]
rs67044678	0.84[EUR][1000 genomes]
rs67261052	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67349960	0.81[ASN][1000 genomes]
rs67784045	0.81[ASN][1000 genomes]
rs68056570	0.81[ASN][1000 genomes]
rs72611185	0.83[EUR][1000 genomes]
rs72611188	0.80[ASN][1000 genomes]
rs7625886	0.85[JPT][hapmap]
rs7636149	0.94[CHB][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs7637009	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7638797	0.96[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7640304	0.81[ASN][1000 genomes]
rs7641135	0.81[EUR][1000 genomes]
rs9343	0.85[JPT][hapmap]
rs9714038	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
7	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
9	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv878175	chr3:195907653-195973244	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv1014159	chr3:195908999-195968512	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
19	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
20	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
22	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
23	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs870339	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL
rs870339	ZDHHC19	cis	cerebellum	SCAN
rs870339	OSTalpha	cis	cerebellum	SCAN
rs870339	SLC51A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195944200-195964000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:195945000-195968400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:195946600-195965600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:195946800-195962600	Weak transcription	Primary T cells from cord blood	blood
5	chr3:195946800-195964200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:195946800-195967400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:195947000-195963800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:195947000-195964000	Weak transcription	Colonic Mucosa	Colon
9	chr3:195947200-195962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:195947200-195962600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:195948000-195970400	Strong transcription	Liver	Liver
12	chr3:195950400-195964400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:195952600-195963200	Weak transcription	K562	blood
14	chr3:195953200-195963800	Weak transcription	Brain Germinal Matrix	brain
15	chr3:195954600-195963800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:195954600-195964600	Weak transcription	Brain Angular Gyrus	brain
17	chr3:195954600-195964800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:195954800-195962800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:195954800-195963800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:195954800-195963800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:195954800-195963800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:195954800-195964600	Weak transcription	NHDF-Ad	bronchial
23	chr3:195954800-195968600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:195955000-195963000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:195955000-195963200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:195955000-195963800	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:195955000-195963800	Weak transcription	HMEC	breast
28	chr3:195955000-195964000	Weak transcription	Fetal Lung	lung
29	chr3:195955200-195963000	Weak transcription	Spleen	Spleen
30	chr3:195955200-195963200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:195955200-195964200	Weak transcription	HSMM	muscle
32	chr3:195955400-195963600	Weak transcription	Gastric	stomach
33	chr3:195955400-195964000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:195955400-195968400	Weak transcription	Pancreas	Pancrea
35	chr3:195955600-195963000	Weak transcription	Left Ventricle	heart
36	chr3:195955600-195963600	Weak transcription	Right Ventricle	heart
37	chr3:195955600-195964200	Weak transcription	HSMMtube	muscle
38	chr3:195956000-195962800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:195956000-195963800	Weak transcription	Placenta	Placenta
40	chr3:195956000-195969800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:195956400-195963600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:195956800-195962400	Weak transcription	Fetal Stomach	stomach
43	chr3:195956800-195963600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:195956800-195963800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr3:195957000-195962600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:195957000-195964200	Weak transcription	Esophagus	oesophagus
47	chr3:195957400-195962400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:195957400-195962600	Weak transcription	Adipose Nuclei	Adipose
49	chr3:195957400-195962800	Weak transcription	NHEK	skin
50	chr3:195957400-195963200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links