Variant report

Variant	rs2028898
Chromosome Location	chr2:85777270-85777271
allele	C/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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85774752..85777473-chr6:30709044..30711134,2	MCF-7	breast:
2	chr2:85776286..85779372-chr2:85843167..85846049,3	K562	blood:
3	chr2:85772605..85778348-chr2:85801967..85806164,7	K562	blood:
4	chr2:85771408..85781005-chr2:85784986..85791406,15	MCF-7	breast:
5	chr2:85647074..85649916-chr2:85775503..85777357,3	MCF-7	breast:
6	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
7	chr2:85657107..85663339-chr2:85772657..85777869,10	MCF-7	breast:
8	chr2:85774772..85777555-chr2:85802674..85804716,2	MCF-7	breast:
9	chr2:85627313..85629571-chr2:85777215..85779946,2	MCF-7	breast:
10	chr2:85641902..85652165-chr2:85771116..85782225,51	MCF-7	breast:
11	chr2:85774425..85777355-chr2:85827588..85829458,2	K562	blood:
12	chr2:85615286..85623438-chr2:85771409..85780547,22	MCF-7	breast:
13	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
14	chr2:85611082..85627761-chr2:85764356..85782623,83	K562	blood:
15	chr2:85564176..85568715-chr2:85772750..85777610,4	K562	blood:
16	chr2:85630277..85634541-chr2:85773340..85777509,4	K562	blood:
17	chr2:85615241..85625394-chr2:85772377..85782714,25	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272273	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000115459	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1009	0.86[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1010	0.85[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs10179195	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10180770	0.84[JPT][hapmap]
rs10182351	0.84[JPT][hapmap]
rs10187424	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap]
rs10198569	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs10206961	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1058588	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1078004	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs11126995	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1124836	0.84[JPT][hapmap]
rs11895341	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895399	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895401	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12473819	0.80[ASN][1000 genomes]
rs12615553	0.86[ASN][1000 genomes]
rs13383605	0.84[JPT][hapmap]
rs1348818	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs14242	0.90[JPT][hapmap]
rs1446669	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1561198	0.86[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1562322	0.90[JPT][hapmap]
rs17026396	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs2028900	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2043675	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044474	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2044475	0.82[TSI][hapmap]
rs2232745	0.84[JPT][hapmap]
rs2232747	0.84[JPT][hapmap]
rs2232750	0.84[JPT][hapmap]
rs2289972	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304564	0.84[JPT][hapmap]
rs2592551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731828	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755008	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755011	0.90[JPT][hapmap]
rs3755015	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3770098	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3821020	0.84[JPT][hapmap]
rs3827550	0.84[JPT][hapmap]
rs55692129	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56819945	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58307667	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs58644336	0.89[ASN][1000 genomes]
rs58768785	0.86[ASN][1000 genomes]
rs60012532	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60788310	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6547621	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs6547622	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6643	0.84[JPT][hapmap]
rs6705971	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs6722691	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731700	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6735663	0.90[ASN][1000 genomes]
rs6738645	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs6743051	0.84[JPT][hapmap]
rs6757263	0.86[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs67988001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs699664	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72643495	0.94[ASN][1000 genomes]
rs73943244	0.85[ASN][1000 genomes]
rs7568458	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7579147	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7579665	0.82[TSI][hapmap]
rs7593969	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605975	0.80[ASN][1000 genomes]
rs7608074	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs762684	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];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2028898	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs2028898	RNF181	cis	parietal	SCAN
rs2028898	VAMP8	cis	uninvolved skin	skin_eQTL
rs2028898	VAMP8	cis	lesional skin	skin_eQTL
rs2028898	GGCX	cis	cerebellum	SCAN
rs2028898	MAT2A	cis	cerebellum	SCAN
rs2028898	VAMP8	cis	multi-tissue	Pritchard
rs2028898	RNF103	cis	parietal	SCAN
rs2028898	VAMP8	cis	lymphoblastoid	seeQTL
rs2028898	VAMP8	cis	parietal	SCAN
rs2028898	GGCX	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85768400-85778000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:85768400-85786600	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:85768600-85779000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr2:85768600-85786200	Strong transcription	Fetal Thymus	thymus
5	chr2:85769400-85782800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:85769400-85786600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:85769400-85786600	Strong transcription	Brain Germinal Matrix	brain
8	chr2:85769400-85787800	Weak transcription	Right Atrium	heart
9	chr2:85769800-85779400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:85769800-85782800	Strong transcription	Thymus	Thymus
11	chr2:85769800-85786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:85769800-85787000	Strong transcription	Fetal Stomach	stomach
13	chr2:85769800-85788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:85770000-85779000	Strong transcription	Liver	Liver
15	chr2:85770000-85783400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:85770200-85787800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:85770400-85779200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:85770400-85786200	Strong transcription	Fetal Intestine Large	intestine
19	chr2:85770400-85786400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:85770600-85779000	Strong transcription	Brain Anterior Caudate	brain
21	chr2:85770600-85781400	Weak transcription	Psoas Muscle	Psoas
22	chr2:85770600-85786400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:85770600-85786600	Strong transcription	Fetal Brain Female	brain
24	chr2:85770800-85778600	Weak transcription	Stomach Mucosa	stomach
25	chr2:85771000-85786400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr2:85771800-85786200	Strong transcription	Fetal Intestine Small	intestine
27	chr2:85772000-85786600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:85772800-85779600	Weak transcription	Right Ventricle	heart
29	chr2:85773000-85778400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:85773200-85777400	Weak transcription	Fetal Lung	lung
31	chr2:85773200-85777400	Weak transcription	HMEC	breast
32	chr2:85773200-85777600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:85773200-85778000	Strong transcription	Brain Hippocampus Middle	brain
34	chr2:85773200-85779000	Weak transcription	Fetal Heart	heart
35	chr2:85773400-85777400	Weak transcription	Ovary	ovary
36	chr2:85773400-85777600	Weak transcription	Small Intestine	intestine
37	chr2:85773400-85777800	Weak transcription	Esophagus	oesophagus
38	chr2:85773400-85780000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:85773400-85786200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:85773600-85777400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:85773600-85777400	Weak transcription	Spleen	Spleen
42	chr2:85773800-85777400	Weak transcription	Gastric	stomach
43	chr2:85774600-85777400	Weak transcription	Brain Substantia Nigra	brain
44	chr2:85774600-85786200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:85775400-85778600	Strong transcription	Brain Angular Gyrus	brain
46	chr2:85775400-85783000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:85775600-85777400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr2:85775600-85777600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:85775600-85777600	Enhancers	NHLF	lung
50	chr2:85775600-85779200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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