Variant report

Variant	rs14242
Chromosome Location	chr2:85820412-85820413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:85820398-85820470	MCF-7	breast:	n/a	n/a
2	CTCF	chr2:85820401-85820488	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr2:85820358-85820473	MCF-7	breast:	n/a	n/a
4	SMC3	chr2:85820272-85820433	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:85819950-85820840	K562	blood:	n/a	n/a
6	CTCF	chr2:85820340-85820490	HepG2	liver:	n/a	n/a
7	RAD21	chr2:85820239-85820564	HepG2	liver:	n/a	n/a
8	MXI1	chr2:85820203-85820581	HepG2	liver:	n/a	n/a
9	CTCF	chr2:85820371-85820485	MCF-7	breast:	n/a	n/a
10	CTCF	chr2:85820210-85820523	HepG2	liver:	n/a	n/a
11	FOXA1	chr2:85820100-85820586	HepG2	liver:	n/a	n/a
12	ZNF217	chr2:85820146-85820481	MCF-7	breast:	n/a	n/a
13	HNF4G	chr2:85820209-85820514	HepG2	liver:	n/a	chr2:85820375-85820390
14	POLR2A	chr2:85820309-85820702	K562	blood:	n/a	n/a
15	MAX	chr2:85820291-85820491	HepG2	liver:	n/a	n/a
16	FOXA2	chr2:85820201-85820494	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:85820086-85820579	Hela-S3	cervix:	n/a	n/a
18	MAFK	chr2:85820228-85820414	HepG2	liver:	n/a	n/a
19	GATA3	chr2:85820108-85820516	MCF-7	breast:	n/a	n/a
20	POLR2A	chr2:85820170-85820739	K562	blood:	n/a	n/a
21	MYC	chr2:85820278-85820509	MCF-7	breast:	n/a	n/a
22	CTCF	chr2:85820377-85820492	MCF-7	breast:	n/a	n/a
23	POLR2A	chr2:85820121-85820646	GM12878	blood:	n/a	n/a
24	CTCF	chr2:85820364-85820477	MCF-7	breast:	n/a	n/a
25	MAX	chr2:85820102-85820648	MCF-7	breast:	n/a	n/a
26	MYC	chr2:85820370-85820438	MCF-7	breast:	n/a	n/a
27	RCOR1	chr2:85820215-85820460	HepG2	liver:	n/a	n/a
28	POLR2A	chr2:85820212-85820749	HepG2	liver:	n/a	n/a
29	MAZ	chr2:85820279-85820479	HepG2	liver:	n/a	n/a
30	RAD21	chr2:85820216-85820531	HepG2	liver:	n/a	n/a
31	NR2F2	chr2:85819944-85820750	MCF-7	breast:	n/a	n/a
32	HNF4A	chr2:85820173-85820585	HepG2	liver:	n/a	chr2:85820376-85820391

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
2	chr2:85820402..85822148-chr2:85985989..85987607,2	K562	blood:
3	chr2:85764880..85767543-chr2:85819729..85822384,2	MCF-7	breast:
4	chr2:85779351..85781176-chr2:85819993..85821834,2	MCF-7	breast:
5	chr2:85765572..85767946-chr2:85820164..85824365,5	MCF-7	breast:

No data

Variant related genes	Relation type
RNF181	TF binding region
ENSG00000115486	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10180770	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10182351	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs10190428	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10191726	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10302	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1044158	0.81[CHD][hapmap]
rs1124836	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13383605	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap];0.90[GIH][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs13418207	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1446669	0.90[JPT][hapmap]
rs1562322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2028898	0.90[JPT][hapmap]
rs2043675	0.90[JPT][hapmap]
rs2118176	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2232745	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2232747	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232750	0.90[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304564	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2592551	0.90[JPT][hapmap]
rs3024831	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs3198089	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3731828	0.84[JPT][hapmap]
rs3755009	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755011	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];0.99[ASN][1000 genomes]
rs3821020	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs3827550	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6643	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6733550	0.81[CHD][hapmap]
rs6743051	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs699664	0.90[JPT][hapmap]
rs7579147	0.84[JPT][hapmap]
rs7593969	0.84[JPT][hapmap]
rs762684	0.90[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs14242	VAMP8	cis	lymphoblastoid	seeQTL
rs14242	LOC388969	cis	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85812600-85821200	Weak transcription	Fetal Heart	heart
2	chr2:85813200-85821400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:85813600-85821400	Weak transcription	Fetal Intestine Large	intestine
4	chr2:85814000-85821600	Weak transcription	Small Intestine	intestine
5	chr2:85815000-85821400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:85815000-85821600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:85815200-85821600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:85815400-85821200	Weak transcription	Dnd41	blood
9	chr2:85815400-85821400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:85815400-85821400	Weak transcription	GM12878-XiMat	blood
11	chr2:85815600-85821400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:85815600-85821400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:85815600-85821400	Weak transcription	Hela-S3	cervix
14	chr2:85815800-85821400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:85815800-85821600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:85816000-85821400	Weak transcription	Fetal Kidney	kidney
17	chr2:85816000-85821400	Weak transcription	Thymus	Thymus
18	chr2:85816200-85821400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:85817600-85821600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:85818200-85821400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:85818200-85821400	Weak transcription	NHEK	skin
22	chr2:85818200-85821600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:85818200-85821600	Enhancers	Pancreas	Pancrea
24	chr2:85818400-85821200	Weak transcription	Liver	Liver
25	chr2:85818400-85821400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:85818400-85821400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:85818400-85821400	Weak transcription	K562	blood
28	chr2:85818400-85821600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:85818400-85821600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:85818400-85821600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:85818400-85821600	Weak transcription	HMEC	breast
32	chr2:85818400-85821800	Weak transcription	Aorta	Aorta
33	chr2:85818600-85821200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:85818600-85821200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:85818600-85821400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:85818600-85821400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:85818800-85821200	Weak transcription	Psoas Muscle	Psoas
38	chr2:85818800-85821400	Weak transcription	Primary B cells from cord blood	blood
39	chr2:85818800-85821400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:85818800-85821400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:85818800-85821400	Weak transcription	HUVEC	blood vessel
42	chr2:85818800-85821600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:85818800-85821800	Genic enhancers	HSMM	muscle
44	chr2:85819000-85820600	Enhancers	Adipose Nuclei	Adipose
45	chr2:85819000-85821000	Weak transcription	Colonic Mucosa	Colon
46	chr2:85819000-85821200	Weak transcription	Right Atrium	heart
47	chr2:85819000-85821400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:85819000-85821400	Weak transcription	Brain Anterior Caudate	brain
49	chr2:85819000-85821400	Weak transcription	Fetal Thymus	thymus
50	chr2:85819000-85821400	Weak transcription	Gastric	stomach

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