Variant report

Variant	rs491166
Chromosome Location	chr3:119387599-119387600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr3:119387275-119387806	SK-N-SH	brain:	n/a	n/a
2	FAM48A	chr3:119387417-119387609	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:119387470-119387931	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119375861..119378454-chr3:119387094..119389806,2	K562	blood:
2	chr3:119366599..119368508-chr3:119385647..119388287,2	MCF-7	breast:
3	chr3:119383319..119384856-chr3:119387419..119389947,2	K562	blood:
4	chr3:119384220..119388638-chr3:119390311..119393902,4	K562	blood:
5	chr3:119387433..119389444-chr3:119393932..119397317,5	K562	blood:
6	chr3:119387339..119389333-chr3:119392737..119395674,3	K562	blood:
7	chr3:119382052..119384819-chr3:119387419..119389641,2	K562	blood:

No data

Variant related genes	Relation type
POPDC2	TF binding region
ENSG00000138495	Chromatin interaction
ENSG00000121577	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1720143	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1806759	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2461826	1.00[JPT][hapmap]
rs2688636	0.88[AFR][1000 genomes]
rs549001	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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	12 gene(s)	inside rSNPs	diseases
5	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
7	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
8	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:119363200-119389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:119367600-119389200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:119367600-119391200	Weak transcription	Fetal Brain Female	brain
13	chr3:119367800-119388800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:119368200-119388200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:119373400-119388800	Weak transcription	Aorta	Aorta
16	chr3:119374800-119389000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:119379200-119391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:119379200-119392400	Weak transcription	Esophagus	oesophagus
19	chr3:119379200-119392400	Weak transcription	Gastric	stomach
20	chr3:119379400-119388600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:119379800-119391800	Weak transcription	Thymus	Thymus
22	chr3:119380000-119391800	Weak transcription	Lung	lung
23	chr3:119380000-119391800	Weak transcription	Ovary	ovary
24	chr3:119380000-119391800	Weak transcription	Pancreas	Pancrea
25	chr3:119380000-119391800	Weak transcription	Spleen	Spleen
26	chr3:119380000-119392000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:119380400-119391000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:119381000-119392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:119381800-119389400	Weak transcription	A549	lung
30	chr3:119382000-119388800	Weak transcription	Right Atrium	heart
31	chr3:119382200-119388000	Weak transcription	Fetal Lung	lung
32	chr3:119382200-119390600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:119382400-119390000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:119382400-119390600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:119382400-119391000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:119382400-119391800	Weak transcription	Fetal Stomach	stomach
37	chr3:119382600-119388800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:119382600-119391800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:119383800-119390600	Weak transcription	Brain Germinal Matrix	brain
40	chr3:119383800-119393800	Strong transcription	Primary B cells from cord blood	blood
41	chr3:119384000-119387600	Weak transcription	NHDF-Ad	bronchial
42	chr3:119384000-119389000	Weak transcription	HSMM	muscle
43	chr3:119384000-119391800	Weak transcription	HSMMtube	muscle
44	chr3:119384000-119395000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr3:119384200-119387800	Active TSS	Right Ventricle	heart
46	chr3:119384200-119391600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr3:119384200-119394400	Weak transcription	Stomach Mucosa	stomach
48	chr3:119384400-119387800	Weak transcription	HMEC	breast
49	chr3:119384400-119388800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:119384400-119391000	Weak transcription	Fetal Intestine Small	intestine

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