Variant report

Variant	rs203474
Chromosome Location	chr17:19854117-19854118
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	SETDB1	chr17:19853790-19854133	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
AKAP10	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12450857	0.84[EUR][1000 genomes]
rs12453720	0.84[EUR][1000 genomes]
rs12943369	0.96[EUR][1000 genomes]
rs1638526	0.97[EUR][1000 genomes]
rs1638527	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1638528	0.95[EUR][1000 genomes]
rs169413	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17604987	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs17605101	0.89[EUR][1000 genomes]
rs17668529	0.81[EUR][1000 genomes]
rs203449	0.94[EUR][1000 genomes]
rs203454	0.95[EUR][1000 genomes]
rs203464	0.93[EUR][1000 genomes]
rs203467	0.96[EUR][1000 genomes]
rs203475	1.00[EUR][1000 genomes]
rs203476	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs203478	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs203480	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2108981	0.89[EUR][1000 genomes]
rs34182788	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34726000	0.89[EUR][1000 genomes]
rs35925051	0.89[EUR][1000 genomes]
rs35979784	0.83[EUR][1000 genomes]
rs36097967	0.88[EUR][1000 genomes]
rs403021	0.90[EUR][1000 genomes]
rs427033	0.88[EUR][1000 genomes]
rs4925055	0.80[EUR][1000 genomes]
rs4925063	0.80[EUR][1000 genomes]
rs4925064	0.81[EUR][1000 genomes]
rs56005410	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62066345	0.81[EUR][1000 genomes]
rs62066346	0.81[EUR][1000 genomes]
rs62066347	0.80[EUR][1000 genomes]
rs62066348	0.81[EUR][1000 genomes]
rs62066349	0.81[EUR][1000 genomes]
rs62066350	0.81[EUR][1000 genomes]
rs62066351	0.81[EUR][1000 genomes]
rs6813	0.93[EUR][1000 genomes]
rs7209653	0.86[EUR][1000 genomes]
rs8079923	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs850622	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9891503	0.96[EUR][1000 genomes]
rs9901294	0.86[EUR][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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs203474	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
2	chr17:19844600-19859200	Weak transcription	NHDF-Ad	bronchial
3	chr17:19844800-19859600	Weak transcription	HSMMtube	muscle
4	chr17:19844800-19861000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr17:19845200-19857200	Weak transcription	Fetal Kidney	kidney
6	chr17:19845400-19857000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:19846800-19875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:19850000-19854600	Strong transcription	Fetal Stomach	stomach
9	chr17:19850600-19855400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:19850600-19861000	Weak transcription	NH-A	brain
11	chr17:19850600-19861400	Weak transcription	Gastric	stomach
12	chr17:19850600-19861600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr17:19850600-19879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr17:19850600-19880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:19850600-19880200	Weak transcription	Aorta	Aorta
16	chr17:19851600-19854200	Weak transcription	Fetal Brain Female	brain
17	chr17:19851600-19858600	Weak transcription	NHEK	skin
18	chr17:19851600-19859200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr17:19851600-19859200	Weak transcription	HSMM	muscle
20	chr17:19851600-19859800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:19851600-19859800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr17:19851600-19871600	Weak transcription	Colonic Mucosa	Colon
23	chr17:19851800-19856000	Weak transcription	Fetal Lung	lung
24	chr17:19851800-19859200	Weak transcription	Osteobl	bone
25	chr17:19852000-19855800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:19852000-19856800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr17:19852000-19857000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr17:19852000-19857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:19852000-19857200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:19852000-19861200	Weak transcription	NHLF	lung
31	chr17:19852000-19871000	Weak transcription	Small Intestine	intestine
32	chr17:19852200-19855000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr17:19852200-19855400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr17:19852200-19855400	Weak transcription	Fetal Intestine Small	intestine
35	chr17:19852200-19855600	Weak transcription	Pancreas	Pancrea
36	chr17:19852200-19856800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:19852200-19856800	Weak transcription	Adipose Nuclei	Adipose
38	chr17:19852200-19856800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr17:19852200-19856800	Weak transcription	Placenta	Placenta
40	chr17:19852200-19857000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr17:19852200-19857000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr17:19852200-19857000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:19852200-19857000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr17:19852200-19857000	Weak transcription	Fetal Muscle Leg	muscle
45	chr17:19852200-19857000	Weak transcription	Lung	lung
46	chr17:19852200-19857000	Weak transcription	Thymus	Thymus
47	chr17:19852200-19857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr17:19852200-19857200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr17:19852200-19858600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:19852200-19858800	Weak transcription	Liver	Liver

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