Variant report

Variant	rs16830984
Chromosome Location	chr2:189855644-189855645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:189855286-189856046	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
COL3A1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10191859	1.00[CEU][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];1.00[EUR][1000 genomes]
rs10201930	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10208311	1.00[CEU][hapmap]
rs10497696	1.00[EUR][1000 genomes]
rs13306260	1.00[EUR][1000 genomes]
rs13425379	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16830969	1.00[CEU][hapmap]
rs16830983	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16831014	1.00[CEU][hapmap]
rs28413125	1.00[EUR][1000 genomes]
rs41263781	1.00[EUR][1000 genomes]
rs41265547	0.84[AFR][1000 genomes]
rs41272837	1.00[EUR][1000 genomes]
rs61112771	1.00[EUR][1000 genomes]
rs6711327	1.00[EUR][1000 genomes]
rs6730236	1.00[CEU][hapmap]
rs6741242	1.00[EUR][1000 genomes]
rs6752549	1.00[EUR][1000 genomes]
rs73047634	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7567045	1.00[EUR][1000 genomes]
rs7600151	1.00[EUR][1000 genomes]
rs7607614	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8224	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459992	chr2:189796272-189855943	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv584057	chr2:189796272-189855943	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875609	chr2:189796272-189862097	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv584058	chr2:189799499-189855943	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	esv1791841	chr2:189811074-189864582	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv584059	chr2:189841052-189868381	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv875612	chr2:189841052-189878769	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv584060	chr2:189844000-189876138	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv584061	chr2:189844000-189878769	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	esv1827498	chr2:189851872-189855943	Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16830984	COL5A2	cis	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189839400-189858000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:189841400-189864000	Weak transcription	Left Ventricle	heart
3	chr2:189841800-189875200	Weak transcription	Colonic Mucosa	Colon
4	chr2:189842400-189866600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:189843400-189861800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:189843600-189874200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:189844400-189866200	Weak transcription	Psoas Muscle	Psoas
8	chr2:189844600-189859000	Weak transcription	Fetal Intestine Small	intestine
9	chr2:189844800-189857200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:189847600-189879200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:189847800-189858600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:189848200-189858000	Weak transcription	Aorta	Aorta
13	chr2:189849400-189877600	Strong transcription	Placenta	Placenta
14	chr2:189849600-189876200	Strong transcription	Stomach Smooth Muscle	stomach
15	chr2:189849800-189856200	Weak transcription	Fetal Stomach	stomach
16	chr2:189849800-189856400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:189849800-189871000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:189850000-189865000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:189850400-189877200	Weak transcription	Right Ventricle	heart
20	chr2:189851800-189859000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:189851800-189862200	Strong transcription	Osteobl	bone
22	chr2:189851800-189863400	Strong transcription	NHDF-Ad	bronchial
23	chr2:189851800-189863800	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr2:189851800-189877200	Strong transcription	Colon Smooth Muscle	Colon
25	chr2:189851800-189878000	Strong transcription	HSMM	muscle
26	chr2:189852000-189856800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:189852000-189856800	Weak transcription	Fetal Kidney	kidney
28	chr2:189852000-189862000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:189852000-189877400	Strong transcription	Adipose Nuclei	Adipose
30	chr2:189852200-189858800	Strong transcription	Fetal Muscle Leg	muscle
31	chr2:189852200-189865800	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr2:189852600-189857600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr2:189852800-189857400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:189853200-189874800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:189853400-189856200	Weak transcription	Ovary	ovary
36	chr2:189853800-189875200	Strong transcription	NHLF	lung
37	chr2:189854000-189878200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:189854200-189876800	Strong transcription	Fetal Lung	lung
39	chr2:189854400-189858800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:189854600-189865200	Strong transcription	HSMMtube	muscle
41	chr2:189855000-189857000	Weak transcription	NH-A	brain
42	chr2:189855200-189856000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:189855600-189872800	Weak transcription	Rectal Mucosa Donor 31	rectum

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