Variant report

Variant	rs6705971
Chromosome Location	chr2:85761417-85761418
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr2:85761408-85761608	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr2:85761335-85761542	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:85761227-85761773	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr2:85761317-85761640	K562	blood:	n/a	n/a
5	MYC	chr2:85761274-85761500	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr2:85761311-85761620	MCF10A-Er-Src	breast:	n/a	n/a

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	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
4	chr2:85642633..85666582-chr2:85757429..85771032,137	MCF-7	breast:

Variant related genes	Relation type
RN7SL830P	TF binding region
MAT2A	TF binding region
ENSG00000273196	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000244399	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1009	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap]
rs1010	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1011	0.87[ASN][1000 genomes]
rs10172544	0.94[ASN][1000 genomes]
rs10175792	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10176176	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187424	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10198569	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10206961	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1058588	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1078004	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11891260	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12473819	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12714145	0.94[ASN][1000 genomes]
rs13394343	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1348818	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1446669	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1561198	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1562323	0.87[ASN][1000 genomes]
rs17026396	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1972297	0.87[ASN][1000 genomes]
rs2028898	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs2028900	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2043675	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs2044474	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]
rs2166529	0.92[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2232748	0.80[JPT][hapmap]
rs2289972	0.90[CHB][hapmap]
rs2366639	0.87[ASN][1000 genomes]
rs2592551	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2886722	0.86[CHB][hapmap]
rs35215812	0.91[ASN][1000 genomes]
rs3731827	0.87[ASN][1000 genomes]
rs3731828	0.90[CHB][hapmap]
rs3755014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770098	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs55971080	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59877521	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547620	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547621	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547624	0.86[ASN][1000 genomes]
rs6547629	0.80[JPT][hapmap]
rs6705839	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6714157	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6714709	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721924	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6731005	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731700	0.81[ASN][1000 genomes]
rs6733550	0.80[JPT][hapmap]
rs6733913	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6735152	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6738009	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6738645	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6739015	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6743030	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750832	0.91[ASN][1000 genomes]
rs6750847	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6757263	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs699664	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7568458	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7579147	0.90[CHB][hapmap]
rs7591175	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7593969	0.90[CHB][hapmap]
rs7605975	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762684	0.90[CHB][hapmap];0.85[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6705971	GGCX	cis	Artery Tibial	GTEx
rs6705971	RNF103	cis	parietal	SCAN
rs6705971	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs6705971	MAT2A	cis	cerebellum	SCAN
rs6705971	VAMP8	cis	parietal	SCAN
rs6705971	VAMP8	cis	multi-tissue	Pritchard
rs6705971	GGCX	cis	Whole Blood	GTEx
rs6705971	GGCX	cis	cerebellum	SCAN
rs6705971	GGCX	cis	Artery Aorta	GTEx
rs6705971	VAMP8	cis	Esophagus Mucosa	GTEx
rs6705971	GGCX	cis	parietal	SCAN
rs6705971	VAMP8	cis	lesional skin	skin_eQTL
rs6705971	VAMP8	cis	uninvolved skin	skin_eQTL
rs6705971	RETSAT	cis	cerebellum	SCAN
rs6705971	VAMP8	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 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	chr2:85758200-85764800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr2:85758600-85761800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:85758600-85762000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:85758600-85764200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:85758800-85761600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:85758800-85763400	Weak transcription	Pancreas	Pancrea
16	chr2:85759200-85764000	Weak transcription	Liver	Liver
17	chr2:85760000-85762800	Enhancers	K562	blood
18	chr2:85760800-85764000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:85761000-85762600	Enhancers	Primary B cells from cord blood	blood
20	chr2:85761200-85764400	Enhancers	Stomach Mucosa	stomach
21	chr2:85761400-85761600	Enhancers	Brain Anterior Caudate	brain
22	chr2:85761400-85761800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:85761400-85761800	Enhancers	NHEK	skin
24	chr2:85761400-85763000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr2:85761400-85763000	Enhancers	Brain Substantia Nigra	brain
26	chr2:85761400-85763200	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr2:85761400-85764400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:85761400-85764600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:85761400-85764600	Enhancers	Primary hematopoietic stem cells	blood

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