Variant report

Variant	rs3755011
Chromosome Location	chr2:85821599-85821600
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr2:85821352-85823520	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:85821253-85823228	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:85821574-85823134	GM12891	blood:	n/a	n/a
4	POLR2A	chr2:85821278-85823600	HUVEC	blood vessel:	n/a	n/a
5	PML	chr2:85821507-85823275	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:85821587-85824943	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:85821118-85823521	K562	blood:	n/a	n/a
8	WRNIP1	chr2:85821575-85822762	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:85821490-85821982	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:85821234-85823184	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr2:85821369-85825652	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:85821358-85821997	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:85821519-85821823	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:85821309-85823251	K562	blood:	n/a	n/a
15	POLR2A	chr2:85821533-85824142	K562	blood:	n/a	n/a
16	RFX5	chr2:85821432-85823573	SK-N-SH	brain:	n/a	chr2:85822709-85822718 chr2:85822788-85822797
17	POLR2A	chr2:85821479-85823246	H1-hESC	embryonic stem cell:	n/a	n/a
18	STAT5A	chr2:85821569-85823273	GM12878	blood:	n/a	chr2:85822185-85822193
19	POLR2A	chr2:85821235-85821946	K562	blood:	n/a	n/a
20	POLR2A	chr2:85821285-85828013	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:85821484-85823489	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:85821591-85821771	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr2:85821319-85823632	HUVEC	blood vessel:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
2	chr1:201984723..201985418-chr2:85821518..85822517,2	Hela-S3	cervix:
3	chr2:85594724..85597082-chr2:85821225..85823571,3	K562	blood:
4	chr2:85647963..85650741-chr2:85821196..85824176,3	K562	blood:
5	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
6	chr2:85646214..85648407-chr2:85821151..85823018,2	K562	blood:
7	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
8	chr2:85820402..85822148-chr2:85985989..85987607,2	K562	blood:
9	chr2:85764880..85767543-chr2:85819729..85822384,2	MCF-7	breast:
10	chr2:74683585..74685846-chr2:85821390..85823281,2	MCF-7	breast:
11	chr2:85779351..85781176-chr2:85819993..85821834,2	MCF-7	breast:
12	chr2:85820787..85822313-chr2:86179412..86182366,2	K562	blood:
13	chr2:85765572..85767946-chr2:85820164..85824365,5	MCF-7	breast:
14	chr2:85788313..85790216-chr2:85821578..85824119,2	K562	blood:
15	chr2:85765237..85769549-chr2:85821409..85826975,10	K562	blood:

No data

Variant related genes	Relation type
RNF181	TF binding region
ENSG00000239779	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000242095	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

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];0.94[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];0.83[ASN][1000 genomes]
rs10302	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1124836	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383605	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap]
rs13418207	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs14242	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]
rs1446669	0.90[JPT][hapmap]
rs1562322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.90[ASN][1000 genomes]
rs2232745	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.92[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	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304564	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2592551	0.90[JPT][hapmap]
rs3024831	1.00[CEU][hapmap]
rs3198089	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3731828	0.84[JPT][hapmap]
rs3755009	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821020	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs3827550	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[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];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6743051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][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	0.85[JPT][hapmap]
rs7593969	0.84[JPT][hapmap]
rs762684	0.90[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3755011	LOC388969	cis	multi-tissue	Pritchard

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85814000-85821600	Weak transcription	Small Intestine	intestine
2	chr2:85815000-85821600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr2:85815200-85821600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:85815800-85821600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:85817600-85821600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:85818200-85821600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:85818200-85821600	Enhancers	Pancreas	Pancrea
8	chr2:85818400-85821600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:85818400-85821600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:85818400-85821600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:85818400-85821600	Weak transcription	HMEC	breast
12	chr2:85818400-85821800	Weak transcription	Aorta	Aorta
13	chr2:85818800-85821600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:85818800-85821800	Genic enhancers	HSMM	muscle
15	chr2:85819000-85821600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:85819000-85821600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:85819200-85821600	Weak transcription	Osteobl	bone
18	chr2:85819200-85821800	Weak transcription	NH-A	brain
19	chr2:85819400-85821600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:85819400-85821600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:85819400-85821800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:85820000-85822000	Enhancers	Esophagus	oesophagus
23	chr2:85820200-85822000	Enhancers	Right Ventricle	heart
24	chr2:85820400-85821600	Weak transcription	Stomach Mucosa	stomach
25	chr2:85820600-85821600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:85820600-85821600	Weak transcription	Adipose Nuclei	Adipose
27	chr2:85820600-85822000	Weak transcription	Ovary	ovary
28	chr2:85820800-85821600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:85821000-85821600	Active TSS	Colonic Mucosa	Colon
30	chr2:85821000-85821800	Weak transcription	HSMMtube	muscle
31	chr2:85821200-85821600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr2:85821200-85821600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:85821200-85821600	Enhancers	Liver	Liver
34	chr2:85821200-85821600	Genic enhancers	Lung	lung
35	chr2:85821200-85821600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:85821200-85821800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr2:85821200-85821800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr2:85821200-85821800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:85821200-85821800	Enhancers	Fetal Heart	heart
40	chr2:85821200-85822000	Enhancers	Fetal Muscle Trunk	muscle
41	chr2:85821200-85822000	Enhancers	Psoas Muscle	Psoas
42	chr2:85821200-85822000	Enhancers	Right Atrium	heart
43	chr2:85821200-85822200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:85821200-85822200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:85821200-85822200	Enhancers	Spleen	Spleen
46	chr2:85821400-85821600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:85821400-85821600	Active TSS	Primary T cells from cord blood	blood
48	chr2:85821400-85821600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:85821400-85821600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr2:85821400-85821600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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