Variant report

Variant	rs3770442
Chromosome Location	chr2:171786239-171786240
allele	A/G
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:171784604..171786258-chr2:171809996..171812623,2	MCF-7	breast:
2	chr2:171784510..171786977-chr2:172014779..172017241,3	K562	blood:
3	chr2:171786011..171788954-chr2:172272838..172276305,3	K562	blood:
4	chr2:171784160..171787954-chr2:172288133..172292253,10	K562	blood:
5	chr2:171626961..171629009-chr2:171784250..171787377,4	K562	blood:
6	chr2:171672408..171674860-chr2:171784778..171786781,3	MCF-7	breast:
7	chr15:72765119..72766854-chr2:171784790..171787087,2	K562	blood:
8	chr2:171785349..171787069-chr2:172015224..172018585,4	MCF-7	breast:
9	chr2:171770723..171773648-chr2:171784124..171786319,2	K562	blood:
10	chr2:171571182..171573160-chr2:171784797..171786624,2	K562	blood:
11	chr2:171770754..171773506-chr2:171785657..171787829,2	K562	blood:
12	chr2:171785493..171786293-chr5:44809583..44810173,2	Hela-S3	cervix:
13	chr2:171784119..171787322-chr2:172288781..172292051,4	MCF-7	breast:
14	chr2:171783791..171787349-chr2:172286549..172291928,9	K562	blood:
15	chr2:171785354..171787093-chr2:172289682..172291292,2	MCF-7	breast:
16	chr2:171627023..171629009-chr2:171784250..171786840,2	K562	blood:
17	chr2:171672439..171674320-chr2:171784947..171786968,2	K562	blood:
18	chr2:171784693..171786944-chr2:172376735..172379477,2	K562	blood:
19	chr2:171786011..171788954-chr2:172274093..172276305,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000071967	Chromatin interaction
ENSG00000112996	Chromatin interaction
ENSG00000261423	Chromatin interaction
ENSG00000235934	Chromatin interaction
ENSG00000115806	Chromatin interaction
ENSG00000204335	Chromatin interaction
ENSG00000198586	Chromatin interaction
ENSG00000128683	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000239467	Chromatin interaction
ENSG00000266020	Chromatin interaction
ENSG00000234350	Chromatin interaction
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10189480	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs10207361	1.00[JPT][hapmap]
rs10210883	0.82[JPT][hapmap]
rs1025240	1.00[CHD][hapmap]
rs1035825	1.00[CHD][hapmap]
rs1035826	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1035828	0.87[CHD][hapmap]
rs1045327	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs10515934	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10803853	0.88[ASN][1000 genomes]
rs10803854	0.82[ASN][1000 genomes]
rs10930446	0.81[ASN][1000 genomes]
rs10930448	0.82[ASN][1000 genomes]
rs10930449	0.82[ASN][1000 genomes]
rs11896607	0.85[ASN][1000 genomes]
rs12471930	0.82[ASN][1000 genomes]
rs12612871	0.82[ASN][1000 genomes]
rs12996518	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12997252	0.95[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs12998296	0.90[CEU][hapmap]
rs13000644	0.81[ASN][1000 genomes]
rs13000898	0.81[AMR][1000 genomes]
rs13001088	0.81[AMR][1000 genomes]
rs13002517	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs13003218	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs13004273	1.00[CHD][hapmap]
rs13008199	1.00[CHD][hapmap]
rs13011011	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13015226	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13016705	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap]
rs13028857	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13035460	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13402107	1.00[JPT][hapmap]
rs13427723	1.00[JPT][hapmap]
rs1344237	1.00[CHD][hapmap]
rs1529378	1.00[CHD][hapmap]
rs1529391	0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs1541781	0.81[ASN][1000 genomes]
rs16859066	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17281735	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1978592	0.87[CHD][hapmap]
rs1991370	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap]
rs2033160	1.00[CHD][hapmap]
rs2195116	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs2356607	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2356608	1.00[CHD][hapmap]
rs2557794	1.00[CHD][hapmap]
rs2676131	1.00[CHD][hapmap]
rs2676151	1.00[CHD][hapmap]
rs34005022	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34330182	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34342928	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34532258	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911788	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35123411	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35230775	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35279794	0.83[ASN][1000 genomes]
rs35890547	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35987434	0.81[AMR][1000 genomes]
rs3755121	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3755125	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770440	1.00[CEU][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770441	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821090	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233833	0.81[ASN][1000 genomes]
rs4564745	1.00[CHD][hapmap]
rs4667666	0.81[ASN][1000 genomes]
rs4668355	0.82[ASN][1000 genomes]
rs4668368	1.00[CHD][hapmap]
rs6433267	0.88[ASN][1000 genomes]
rs6433276	1.00[CHD][hapmap]
rs6710035	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6714164	1.00[CHD][hapmap]
rs6714300	0.82[ASN][1000 genomes]
rs6715386	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6716127	1.00[CHD][hapmap]
rs6724493	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6729847	0.88[ASN][1000 genomes]
rs6730417	1.00[CHD][hapmap]
rs6742797	0.82[ASN][1000 genomes]
rs6758331	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs6761642	1.00[CHD][hapmap]
rs6761759	0.95[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs6761889	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs71415229	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71415231	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71415232	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71415233	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs731692	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs731693	0.82[ASN][1000 genomes]
rs73976229	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7570701	0.82[ASN][1000 genomes]
rs7587244	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs919190	0.85[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	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3770442	SP5	cis	cerebellum	SCAN
rs3770442	FADS2	trans	cerebellum	SCAN
rs3770442	TLK1	cis	uninvolved skin	skin_eQTL
rs3770442	TLK1	cis	normal skin	skin_eQTL
rs3770442	TLK1	cis	lesional skin	skin_eQTL
rs3770442	TLK1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171784400-171787000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr2:171784400-171787600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:171784800-171786600	Active TSS	Brain Germinal Matrix	brain
4	chr2:171784800-171786800	Active TSS	Colon Smooth Muscle	Colon
5	chr2:171784800-171786800	Active TSS	Fetal Kidney	kidney
6	chr2:171784800-171787000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr2:171784800-171787400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:171784800-171787600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:171785000-171786400	Active TSS	Primary hematopoietic stem cells	blood
10	chr2:171785000-171786800	Active TSS	Gastric	stomach
11	chr2:171785000-171787000	Bivalent/Poised TSS	HepG2	liver
12	chr2:171785000-171787200	Active TSS	Stomach Mucosa	stomach
13	chr2:171785000-171787200	Active TSS	A549	lung
14	chr2:171785000-171787400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:171785000-171787400	Active TSS	Left Ventricle	heart
16	chr2:171785200-171786400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:171785200-171786400	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr2:171785200-171786400	Active TSS	Stomach Smooth Muscle	stomach
19	chr2:171785200-171786600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:171785200-171786600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr2:171785200-171786600	Active TSS	Liver	Liver
22	chr2:171785200-171786600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr2:171785200-171786600	Active TSS	Brain Substantia Nigra	brain
24	chr2:171785200-171786600	Active TSS	Fetal Stomach	stomach
25	chr2:171785200-171786600	Active TSS	Placenta Amnion	Placenta Amnion
26	chr2:171785200-171786600	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr2:171785200-171786800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr2:171785200-171786800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr2:171785200-171786800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:171785200-171786800	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr2:171785200-171786800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:171785200-171786800	Active TSS	Aorta	Aorta
33	chr2:171785200-171786800	Active TSS	Brain Anterior Caudate	brain
34	chr2:171785200-171786800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:171785200-171786800	Active TSS	Fetal Intestine Large	intestine
36	chr2:171785200-171786800	Active TSS	Psoas Muscle	Psoas
37	chr2:171785200-171786800	Active TSS	Right Ventricle	heart
38	chr2:171785200-171786800	Active TSS	Dnd41	blood
39	chr2:171785200-171786800	Active TSS	K562	blood
40	chr2:171785200-171787000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:171785200-171787000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:171785200-171787000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:171785200-171787000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:171785200-171787000	Active TSS	Fetal Heart	heart
45	chr2:171785200-171787000	Active TSS	Fetal Lung	lung
46	chr2:171785200-171787200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:171785200-171787200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr2:171785200-171787200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:171785200-171787200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:171785200-171787200	Active TSS	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links