Variant report

Variant	rs2274993
Chromosome Location	chr1:154209490-154209491
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154190796..154197109-chr1:154207892..154217963,21	MCF-7	breast:
2	chr1:154207955..154211164-chr1:154212760..154216262,4	MCF-7	breast:
3	chr1:154153510..154155869-chr1:154207708..154210677,2	MCF-7	breast:
4	chr1:154208334..154210712-chr1:154220041..154222469,3	MCF-7	breast:
5	chr1:154201106..154203777-chr1:154208596..154211363,2	K562	blood:
6	chr1:154209373..154211849-chr1:154214805..154217325,2	K562	blood:
7	chr1:154192348..154196055-chr1:154207328..154211184,7	MCF-7	breast:
8	chr1:154199628..154201203-chr1:154208732..154211600,2	MCF-7	breast:
9	chr1:154202277..154205016-chr1:154208534..154211363,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143549	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10158820	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1044013	0.80[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11265238	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs11265251	0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11265425	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs11802893	0.81[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs1194593	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1194596	0.81[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12023901	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12025237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026177	0.81[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs12026615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12028554	0.86[ASN][1000 genomes]
rs12028949	0.81[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs12043131	0.91[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.83[AFR][1000 genomes]
rs12062977	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12135346	0.88[ASN][1000 genomes]
rs12733060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742691	0.87[ASN][1000 genomes]
rs12743874	0.89[ASN][1000 genomes]
rs12749447	0.88[ASN][1000 genomes]
rs12750321	0.89[ASN][1000 genomes]
rs16835846	0.81[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs16835852	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs1760801	0.82[ASN][1000 genomes]
rs1760802	0.95[JPT][hapmap]
rs1986709	0.85[ASN][1000 genomes]
rs2282227	0.96[ASN][1000 genomes]
rs2340473	0.83[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2790689	0.82[JPT][hapmap]
rs28372838	0.80[EUR][1000 genomes]
rs2879788	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs34128679	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34335016	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34752019	0.82[JPT][hapmap]
rs35761479	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3762339	0.87[ASN][1000 genomes]
rs3762340	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3790613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811453	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3811455	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs3828077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935419	0.81[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs4240871	0.86[ASN][1000 genomes]
rs4459102	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs4620534	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs6427509	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6657214	0.86[ASN][1000 genomes]
rs6671009	0.82[JPT][hapmap]
rs6673752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676022	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6719	0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7517578	0.84[ASN][1000 genomes]
rs9803857	0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9943093	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers 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	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription 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 miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2274993	RAB13	cis	parietal	SCAN
rs2274993	HAX1	cis	cerebellum	SCAN
rs2274993	DENND4B	cis	parietal	SCAN
rs2274993	PIP5K1A	cis	cerebellum	SCAN
rs2274993	C1orf43	cis	parietal	SCAN
rs2274993	HAX1	cis	lymphoblastoid	seeQTL
rs2274993	SLC27A3	cis	lymphoblastoid	seeQTL
rs2274993	SCAMP3	cis	parietal	SCAN
rs2274993	HAX1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154195200-154211400	Weak transcription	Right Atrium	heart
2	chr1:154195400-154234600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:154196400-154218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:154196600-154237600	Strong transcription	Fetal Thymus	thymus
8	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:154196800-154211800	Strong transcription	NHEK	skin
10	chr1:154196800-154224200	Strong transcription	K562	blood
11	chr1:154196800-154224400	Strong transcription	Primary B cells from cord blood	blood
12	chr1:154196800-154235800	Strong transcription	HUVEC	blood vessel
13	chr1:154196800-154242600	Strong transcription	A549	lung
14	chr1:154197000-154235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:154197200-154210800	Strong transcription	HMEC	breast
21	chr1:154197200-154214200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:154197400-154212200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:154197400-154224200	Strong transcription	Hela-S3	cervix
26	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
27	chr1:154197600-154209600	Strong transcription	Fetal Intestine Small	intestine
28	chr1:154197600-154210600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:154197600-154211200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:154197600-154211200	Strong transcription	Lung	lung
31	chr1:154197600-154212800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:154197600-154213200	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr1:154197600-154214000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:154197600-154214600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:154197600-154218600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:154197600-154218800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:154197600-154226400	Strong transcription	Osteobl	bone
38	chr1:154197600-154236000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:154197600-154236200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:154197600-154236800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:154197600-154239200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:154197600-154239200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:154197600-154239400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:154197600-154239800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:154197600-154239800	Strong transcription	NHLF	lung
46	chr1:154197600-154242000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:154197600-154243000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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