Variant report

Variant	rs2592551
Chromosome Location	chr2:85780131-85780132
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85779375..85781145-chr2:85838593..85840325,2	MCF-7	breast:
2	chr2:85645601..85649327-chr2:85777526..85783021,9	MCF-7	breast:
3	chr2:85771408..85781005-chr2:85784986..85791406,15	MCF-7	breast:
4	chr2:85580097..85583436-chr2:85778149..85781015,4	MCF-7	breast:
5	chr2:85777446..85780419-chr2:85822995..85825315,2	MCF-7	breast:
6	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
7	chr2:85641902..85652165-chr2:85771116..85782225,51	MCF-7	breast:
8	chr2:85615286..85623438-chr2:85771409..85780547,22	MCF-7	breast:
9	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
10	chr2:85611082..85627761-chr2:85764356..85782623,83	K562	blood:
11	chr2:85779358..85780862-chr2:85821537..85824017,2	MCF-7	breast:
12	chr2:85624011..85626012-chr2:85777825..85780459,3	MCF-7	breast:
13	chr2:85779865..85782682-chr2:85803471..85805138,2	MCF-7	breast:
14	chr2:85615241..85625394-chr2:85772377..85782714,25	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000042445	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000252293	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1009	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs1010	0.85[CHB][hapmap];0.83[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];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs10198569	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs10206961	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap]
rs1058588	0.86[CHB][hapmap];0.82[CHD][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];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1124836	0.84[JPT][hapmap]
rs11895341	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895399	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895401	0.93[AFR][1000 genomes];0.84[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];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1561198	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs1562322	0.90[JPT][hapmap]
rs17026396	0.90[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap]
rs2028898	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]
rs2028900	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2043675	0.93[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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044474	0.90[CHB][hapmap];0.85[JPT][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];0.94[MEX][hapmap];0.95[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]
rs3731828	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[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]
rs4258795	0.81[TSI][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];0.95[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];0.85[JPT][hapmap]
rs6722691	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731700	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.83[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	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[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];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7593969	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[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];0.89[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2592551	VAMP8	cis	multi-tissue	Pritchard
rs2592551	VAMP8	cis	uninvolved skin	skin_eQTL
rs2592551	GGCX	cis	multi-tissue	Pritchard
rs2592551	GGCX	cis	parietal	SCAN
rs2592551	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs2592551	VAMP8	cis	lymphoblastoid	seeQTL
rs2592551	RNF181	cis	parietal	SCAN
rs2592551	RNF103	cis	parietal	SCAN
rs2592551	VAMP8	cis	parietal	SCAN
rs2592551	VAMP8	cis	lesional skin	skin_eQTL
rs2592551	MAT2A	cis	cerebellum	SCAN
rs2592551	GGCX	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85768400-85786600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr2:85768600-85786200	Strong transcription	Fetal Thymus	thymus
3	chr2:85769400-85782800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:85769400-85786600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:85769400-85786600	Strong transcription	Brain Germinal Matrix	brain
6	chr2:85769400-85787800	Weak transcription	Right Atrium	heart
7	chr2:85769800-85782800	Strong transcription	Thymus	Thymus
8	chr2:85769800-85786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:85769800-85787000	Strong transcription	Fetal Stomach	stomach
10	chr2:85769800-85788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:85770000-85783400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:85770200-85787800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:85770400-85786200	Strong transcription	Fetal Intestine Large	intestine
14	chr2:85770400-85786400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:85770600-85781400	Weak transcription	Psoas Muscle	Psoas
16	chr2:85770600-85786400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:85770600-85786600	Strong transcription	Fetal Brain Female	brain
18	chr2:85771000-85786400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:85771800-85786200	Strong transcription	Fetal Intestine Small	intestine
20	chr2:85772000-85786600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:85773400-85786200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:85774600-85786200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:85775400-85783000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:85775600-85786600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:85775800-85783400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:85776200-85782800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:85776200-85785000	Strong transcription	HepG2	liver
28	chr2:85776200-85786000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:85776200-85786400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:85776200-85786400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr2:85776400-85783200	Strong transcription	Colon Smooth Muscle	Colon
32	chr2:85776600-85782800	Strong transcription	Aorta	Aorta
33	chr2:85776600-85784000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:85776600-85787000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:85776800-85784200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:85776800-85785000	Strong transcription	Dnd41	blood
37	chr2:85776800-85786200	Strong transcription	Primary T cells from cord blood	blood
38	chr2:85777000-85782600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr2:85777000-85782600	Strong transcription	Fetal Brain Male	brain
40	chr2:85777000-85782800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:85777000-85783400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:85777000-85783400	Strong transcription	Colonic Mucosa	Colon
43	chr2:85777000-85784000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr2:85777000-85784000	Strong transcription	Left Ventricle	heart
45	chr2:85777000-85784400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:85777000-85785800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:85777000-85786200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:85777000-85786400	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr2:85777000-85786400	Strong transcription	Lung	lung
50	chr2:85777000-85787200	Strong transcription	NHEK	skin

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