Variant report

Variant	rs2044474
Chromosome Location	chr2:85758790-85758791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85644216..85654950-chr2:85758513..85769717,70	MCF-7	breast:
2	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
3	chr2:85642633..85666582-chr2:85757429..85771032,137	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252293	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000152292	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1009	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1010	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1011	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10172544	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10175792	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10176176	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10179195	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10187424	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10198569	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10206961	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1058588	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1078004	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11891260	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11895341	0.81[ASN][1000 genomes]
rs11895399	0.81[ASN][1000 genomes]
rs11895401	0.81[ASN][1000 genomes]
rs12473819	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12714145	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13394343	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411109	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1348818	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1446669	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1561198	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1562323	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17026396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972297	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2028898	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2028900	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2043675	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2166529	0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs2232748	0.81[JPT][hapmap]
rs2289972	0.90[CHB][hapmap]
rs2366639	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2592551	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2886722	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs35215812	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35565292	0.82[AMR][1000 genomes]
rs3731827	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3731828	0.90[CHB][hapmap]
rs3755014	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755015	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770098	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55971080	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56819945	0.81[ASN][1000 genomes]
rs59877521	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547620	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547621	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547624	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6547629	0.80[JPT][hapmap]
rs6705839	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6705971	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6714157	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6714709	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721924	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6722691	0.81[ASN][1000 genomes]
rs6731005	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6731700	0.80[ASN][1000 genomes]
rs6733550	0.80[JPT][hapmap]
rs6733913	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735152	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6738645	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6739015	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743030	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750832	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6750847	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757263	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs699664	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7568458	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7579147	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7591175	0.87[CHB][hapmap];0.81[AMR][1000 genomes]
rs7593969	0.90[CHB][hapmap]
rs7605975	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762684	0.91[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2044474	GGCX	cis	Nerve Tibial	GTEx
rs2044474	GGCX	cis	Artery Tibial	GTEx
rs2044474	GGCX	cis	Artery Aorta	GTEx
rs2044474	VAMP8	cis	uninvolved skin	skin_eQTL
rs2044474	VAMP8	cis	multi-tissue	Pritchard
rs2044474	GGCX	cis	Whole Blood	GTEx
rs2044474	GGCX	Cis_1M	lymphoblastoid	RTeQTL
rs2044474	VAMP8	cis	Esophagus Mucosa	GTEx
rs2044474	VAMP8	cis	lesional skin	skin_eQTL
rs2044474	VAMP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85734600-85762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
3	chr2:85751200-85764000	Weak transcription	Psoas Muscle	Psoas
4	chr2:85751200-85764400	Weak transcription	Small Intestine	intestine
5	chr2:85752000-85764800	Weak transcription	Gastric	stomach
6	chr2:85752400-85764800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:85752600-85763600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:85752800-85761600	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:85753000-85764000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:85753200-85761000	Weak transcription	Primary B cells from cord blood	blood
11	chr2:85758200-85758800	Enhancers	Brain Anterior Caudate	brain
12	chr2:85758200-85758800	Enhancers	Brain Cingulate Gyrus	brain
13	chr2:85758200-85758800	Enhancers	Brain Substantia Nigra	brain
14	chr2:85758200-85758800	Enhancers	Pancreas	Pancrea
15	chr2:85758200-85759200	Enhancers	Liver	Liver
16	chr2:85758200-85764800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr2:85758400-85758800	Enhancers	Stomach Mucosa	stomach
18	chr2:85758600-85761800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:85758600-85762000	Weak transcription	Brain Angular Gyrus	brain
20	chr2:85758600-85764200	Weak transcription	Duodenum Mucosa	Duodenum

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