Variant report

Variant	rs11642862
Chromosome Location	chr16:30785824-30785825
allele	C/T
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:18)
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	POLR2A	chr16:30785470-30787757	K562	blood:	n/a	n/a
2	POLR2A	chr16:30785393-30787718	K562	blood:	n/a	n/a
3	POLR2A	chr16:30785790-30788431	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr16:30785499-30785931	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr16:30785774-30792079	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr16:30785485-30787788	GM12892	blood:	n/a	n/a
7	POLR2A	chr16:30785771-30786006	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:30785553-30792383	K562	blood:	n/a	n/a
9	POLR2A	chr16:30782383-30800309	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:30785046-30787693	HepG2	liver:	n/a	n/a
11	POLR2A	chr16:30785676-30787759	K562	blood:	n/a	n/a
12	MAX	chr16:30785804-30787753	HepG2	liver:	n/a	n/a
13	POLR2A	chr16:30785583-30787852	GM12892	blood:	n/a	n/a
14	POLR2A	chr16:30785714-30787699	GM12891	blood:	n/a	n/a
15	POLR2A	chr16:30785728-30786015	GM12878	blood:	n/a	n/a
16	POLR2A	chr16:30785463-30787779	HL-60	blood:	n/a	n/a
17	POLR2A	chr16:30785480-30792632	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr16:30785760-30787733	GM12892	blood:	n/a	n/a
19	POLR2A	chr16:30782939-30789605	GM12878	blood:	n/a	n/a
20	POLR2A	chr16:30784849-30787729	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr16:30785621-30787731	K562	blood:	n/a	n/a
22	POLR2A	chr16:30785723-30785875	A549	lung:	n/a	n/a
23	POLR2A	chr16:30785815-30786011	GM12878	blood:	n/a	n/a
24	POLR2A	chr16:30785795-30787667	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr16:30785541-30785840	GM12891	blood:	n/a	n/a
26	POLR2A	chr16:30785626-30787707	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr16:30785657-30787629	HepG2	liver:	n/a	n/a
28	POLR2A	chr16:30785692-30786095	HepG2	liver:	n/a	n/a
29	USF2	chr16:30785659-30787621	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr16:30785766-30786297	K562	blood:	n/a	n/a
31	POLR2A	chr16:30785802-30786130	GM12891	blood:	n/a	n/a
32	POLR2A	chr16:30785609-30791013	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30785578..30788254-chr16:30911758..30913330,2	K562	blood:
2	chr16:30785755..30789519-chr16:30993933..30997614,3	K562	blood:
3	chr16:30785759..30789223-chr16:30822658..30825886,4	K562	blood:
4	chr16:30668135..30670286-chr16:30783767..30786640,2	K562	blood:
5	chr16:30785822..30789729-chr16:30809078..30811832,3	K562	blood:
6	chr16:30785797..30787464-chr16:30963811..30966272,2	MCF-7	breast:
7	chr16:30785225..30786834-chr16:30968758..30970807,2	K562	blood:
8	chr16:30783772..30791593-chr16:30931071..30936822,9	MCF-7	breast:
9	chr16:30785469..30788117-chr2:27975915..27977847,2	MCF-7	breast:
10	chr16:30785189..30790485-chr16:30931540..30936077,12	K562	blood:
11	chr16:30756700..30760166-chr16:30785453..30788232,3	MCF-7	breast:
12	chr16:30784974..30791554-chr16:30930641..30936449,8	MCF-7	breast:
13	chr16:30749452..30756542-chr16:30785692..30792123,12	MCF-7	breast:
14	chr16:30707557..30712450-chr16:30785751..30791890,10	K562	blood:
15	chr16:30785425..30787297-chr16:31190494..31192652,2	K562	blood:
16	chr16:30707849..30711301-chr16:30785397..30790684,8	K562	blood:
17	chr16:30671278..30673717-chr16:30785023..30788710,4	MCF-7	breast:
18	chr16:30785189..30790485-chr16:30931540..30935208,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000262026	TF binding region
ENSG00000260852	Chromatin interaction
ENSG00000099364	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000268863	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000099377	Chromatin interaction
ENSG00000099381	Chromatin interaction
ENSG00000156873	Chromatin interaction
ENSG00000260899	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11642466	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11642603	1.00[CEU][hapmap]
rs11642733	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11645175	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs11645367	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11647243	0.88[CEU][hapmap];1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
7	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
8	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
9	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
10	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
11	nsv9438	chr16:30770203-30799442	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11642862	NCRNA00095	cis	cerebellum	SCAN
rs11642862	DCTPP1	cis	cerebellum	SCAN
rs11642862	RABEP2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30774200-30786600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:30774600-30786200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr16:30774800-30786200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr16:30774800-30786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr16:30775000-30786000	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr16:30775000-30786000	Strong transcription	NH-A	brain
7	chr16:30775000-30786200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:30775000-30786200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr16:30775000-30786200	Strong transcription	Fetal Thymus	thymus
10	chr16:30775000-30786400	Strong transcription	Thymus	Thymus
11	chr16:30775200-30786000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr16:30775200-30786000	Strong transcription	Primary hematopoietic stem cells	blood
13	chr16:30775200-30786000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr16:30775200-30786000	Strong transcription	HUVEC	blood vessel
15	chr16:30775200-30786000	Strong transcription	NHLF	lung
16	chr16:30775200-30786200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr16:30775200-30786200	Strong transcription	A549	lung
18	chr16:30775400-30786000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr16:30775400-30786000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr16:30775400-30786000	Strong transcription	Primary T cells from cord blood	blood
21	chr16:30775400-30786000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr16:30775400-30786000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr16:30775400-30786000	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr16:30775400-30786000	Strong transcription	Fetal Lung	lung
25	chr16:30775400-30786000	Strong transcription	Osteobl	bone
26	chr16:30775400-30786200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr16:30775400-30786200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:30775400-30786200	Strong transcription	Fetal Intestine Large	intestine
29	chr16:30775400-30786200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr16:30775600-30786000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr16:30775600-30786000	Strong transcription	Brain Cingulate Gyrus	brain
32	chr16:30775600-30786000	Strong transcription	Brain Hippocampus Middle	brain
33	chr16:30775600-30786000	Strong transcription	Fetal Stomach	stomach
34	chr16:30775600-30786200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr16:30775600-30786200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr16:30775800-30786000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr16:30775800-30786000	Strong transcription	Brain Germinal Matrix	brain
38	chr16:30775800-30786000	Strong transcription	Esophagus	oesophagus
39	chr16:30775800-30786200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr16:30775800-30786200	Strong transcription	Rectal Smooth Muscle	rectum
41	chr16:30776000-30786000	Strong transcription	Ovary	ovary
42	chr16:30776000-30786200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr16:30776400-30786000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr16:30776800-30786200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr16:30778200-30786000	Strong transcription	Lung	lung
46	chr16:30778200-30786400	Weak transcription	Right Atrium	heart
47	chr16:30780800-30786200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr16:30781200-30786200	Weak transcription	Stomach Mucosa	stomach
49	chr16:30781200-30786400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr16:30781400-30786000	Strong transcription	Primary B cells from peripheral blood	blood

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