Variant report

Variant	rs2954742
Chromosome Location	chr17:15451584-15451585
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	chr17:15451523-15451642	A549	lung:	n/a	n/a

Variant related genes	Relation type
TVP23C	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs189330	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs190206	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2270136	0.92[ASN][1000 genomes]
rs236804	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs236815	0.84[EUR][1000 genomes]
rs2907502	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2938158	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2938170	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2938171	0.90[ASN][1000 genomes]
rs2954739	0.80[ASN][1000 genomes]
rs483702	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58393633	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv960418	chr17:15441505-15470653	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3395445	chr17:15444877-15459575	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv457695	chr17:15447364-15611495	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv574462	chr17:15447364-15611495	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	esv3434152	chr17:15450327-15455625	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
12	esv3508601	chr17:15450327-15459525	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv3508602	chr17:15450327-15459525	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2954742	AC005517.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2954742	AC005517.3	cis	Thyroid	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383400-15455000	Weak transcription	Gastric	stomach
2	chr17:15416200-15466000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr17:15417600-15466400	Weak transcription	Ovary	ovary
4	chr17:15420400-15452800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:15420600-15459600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr17:15421200-15453000	Weak transcription	Aorta	Aorta
7	chr17:15421800-15465600	Weak transcription	Hela-S3	cervix
8	chr17:15422800-15465800	Weak transcription	Fetal Intestine Small	intestine
9	chr17:15429800-15466000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:15429800-15466400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr17:15431000-15465400	Weak transcription	K562	blood
12	chr17:15439000-15466000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:15439600-15456000	Weak transcription	Colon Smooth Muscle	Colon
14	chr17:15439600-15466000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:15439800-15466400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr17:15440200-15466400	Weak transcription	Left Ventricle	heart
17	chr17:15440800-15466000	Weak transcription	NHEK	skin
18	chr17:15441000-15466000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr17:15442600-15465400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr17:15442600-15466000	Weak transcription	A549	lung
21	chr17:15442600-15466400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr17:15442800-15462600	Weak transcription	Thymus	Thymus
23	chr17:15442800-15465800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:15442800-15466400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:15442800-15466400	Weak transcription	Lung	lung
26	chr17:15444200-15452200	Weak transcription	GM12878-XiMat	blood
27	chr17:15444200-15452400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr17:15445200-15462000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr17:15447200-15453000	Weak transcription	Esophagus	oesophagus
30	chr17:15447200-15465200	Weak transcription	HUVEC	blood vessel
31	chr17:15449000-15453000	Weak transcription	Fetal Intestine Large	intestine
32	chr17:15449000-15455000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr17:15449000-15465200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:15449000-15466000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:15449000-15466000	Weak transcription	Brain Anterior Caudate	brain
36	chr17:15449000-15466000	Weak transcription	HSMMtube	muscle
37	chr17:15449200-15452200	Weak transcription	Brain Substantia Nigra	brain
38	chr17:15449200-15454600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:15449200-15454800	Weak transcription	Fetal Muscle Leg	muscle
40	chr17:15449200-15459200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr17:15449200-15465400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr17:15449200-15466000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr17:15449200-15466000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr17:15449200-15466000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr17:15449200-15466000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr17:15449200-15466000	Weak transcription	NH-A	brain
47	chr17:15449400-15453000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr17:15449400-15454200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr17:15449400-15458600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:15449400-15462800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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