Variant report

Variant	rs11693759
Chromosome Location	chr2:128601766-128601767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:128600356-128602181	K562	blood:	n/a	n/a
2	POLR2A	chr2:128600454-128602353	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr2:128601150-128601821	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:128601481-128602214	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:128601084-128601981	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr2:128600610-128602172	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:128601665-128602816	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr2:128601714-128602312	HCT-116	colon:	n/a	n/a
9	POLR2A	chr2:128600372-128602060	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr2:128601074-128603496	GM12892	blood:	n/a	n/a
11	POLR2A	chr2:128601321-128601867	K562	blood:	n/a	n/a
12	POLR2A	chr2:128599342-128603627	K562	blood:	n/a	n/a
13	POLR2A	chr2:128601215-128603261	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:128601606-128601812	HCT-116	colon:	n/a	n/a
15	POLR2A	chr2:128600490-128602220	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:128601732-128602167	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr2:128601490-128601876	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr2:128601745-128601814	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr2:128600436-128602335	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:128601075-128602279	K562	blood:	n/a	n/a
21	POLR2A	chr2:128600565-128602208	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:128599246-128604171	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:128600810..128606151-chr2:128613987..128618367,4	MCF-7	breast:
2	chr2:128600996..128603180-chr2:128603280..128605705,2	MCF-7	breast:
3	chr2:128586393..128588359-chr2:128599372..128601896,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POLR2D-1	chr2:128601127-128603261	ENSG00000270081.1

No data

Variant related genes	Relation type
RNU6-395P	TF binding region
ENSG00000144231	Chromatin interaction
ENSG00000244563	Chromatin interaction
ENSG00000200390	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10171898	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210695	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11557685	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11674513	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678032	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11692524	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13397060	1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13421835	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13423029	0.81[ASN][1000 genomes]
rs17418125	1.00[ASN][1000 genomes]
rs17534053	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17534123	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17599575	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17600177	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3771291	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56954978	1.00[ASN][1000 genomes]
rs57410763	0.86[ASN][1000 genomes]
rs57498556	1.00[ASN][1000 genomes]
rs57913162	1.00[ASN][1000 genomes]
rs57986825	1.00[ASN][1000 genomes]
rs58080260	1.00[ASN][1000 genomes]
rs59009188	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs59090605	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59727076	1.00[ASN][1000 genomes]
rs59918187	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs60087786	1.00[ASN][1000 genomes]
rs61187878	1.00[ASN][1000 genomes]
rs61730415	1.00[ASN][1000 genomes]
rs6714620	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6734925	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756507	1.00[ASN][1000 genomes]
rs72963794	1.00[ASN][1000 genomes]
rs7560482	0.81[ASN][1000 genomes]
rs7574303	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7575961	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7585200	1.00[ASN][1000 genomes]
rs7591477	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7605158	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368061	chr2:128375044-128672849	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11693759	WDR33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128588000-128602600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:128588000-128602600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:128588800-128602600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:128589000-128604000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:128589200-128602400	Weak transcription	HMEC	breast
6	chr2:128589200-128602600	Weak transcription	Thymus	Thymus
7	chr2:128589200-128605400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:128589600-128602000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:128590200-128602000	Weak transcription	Primary B cells from cord blood	blood
10	chr2:128590200-128603400	Weak transcription	Spleen	Spleen
11	chr2:128590400-128602600	Weak transcription	Liver	Liver
12	chr2:128590800-128604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:128591000-128602000	Weak transcription	GM12878-XiMat	blood
14	chr2:128593800-128604200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:128594200-128602600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:128594200-128602600	Weak transcription	Fetal Brain Female	brain
17	chr2:128596400-128602000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:128596800-128603400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:128597000-128602600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:128597200-128601800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:128597600-128602400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:128597600-128604000	Weak transcription	HSMMtube	muscle
23	chr2:128598400-128602600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:128598600-128602400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:128598600-128602600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:128598800-128602400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:128598800-128602600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:128598800-128602600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:128599000-128602000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:128599000-128602600	Weak transcription	Lung	lung
31	chr2:128599200-128602000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:128599200-128602600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:128599200-128604200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:128599200-128604200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:128599400-128602200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:128599400-128602400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:128599400-128602600	Weak transcription	Primary T cells from cord blood	blood
38	chr2:128599400-128604000	Weak transcription	Colonic Mucosa	Colon
39	chr2:128599400-128604400	Weak transcription	Fetal Brain Male	brain
40	chr2:128599600-128602200	Weak transcription	Fetal Intestine Large	intestine
41	chr2:128599600-128602600	Weak transcription	K562	blood
42	chr2:128599600-128604000	Weak transcription	HepG2	liver
43	chr2:128599800-128601800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:128599800-128602000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:128599800-128602600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:128600000-128602000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:128600000-128602200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:128600000-128602200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:128600000-128602600	Weak transcription	NHEK	skin
50	chr2:128600000-128602800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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