Variant report

Variant	rs175921
Chromosome Location	chr17:19854918-19854919
allele	C/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	NR2F2	chr17:19854783-19855228	K562	blood:	n/a	n/a
2	NR2F2	chr17:19854815-19855207	K562	blood:	n/a	n/a
3	NR3C1	chr17:19854910-19855247	A549	lung:	n/a	n/a
4	NR3C1	chr17:19854822-19855211	A549	lung:	n/a	n/a

Variant related genes	Relation type
AKAP10	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11204419	0.90[ASN][1000 genomes]
rs11204420	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11204421	0.80[ASN][1000 genomes]
rs119672	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1479129	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1638525	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169412	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169414	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs175922	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs191865	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203450	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203451	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203452	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203455	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs203456	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203457	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203458	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203459	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs203460	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203461	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203462	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203465	0.93[ASN][1000 genomes]
rs203466	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203469	0.84[ASN][1000 genomes]
rs203470	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203477	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203479	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203481	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203482	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2108978	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs397969	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4925060	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56153261	0.83[ASN][1000 genomes]
rs6587206	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7222403	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8066150	0.93[ASN][1000 genomes]
rs850623	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860335	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9907752	0.89[ASN][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
rs175921	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 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	chr17:19850600-19855400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:19850600-19861000	Weak transcription	NH-A	brain
10	chr17:19850600-19861400	Weak transcription	Gastric	stomach
11	chr17:19850600-19861600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr17:19850600-19879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr17:19850600-19880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:19850600-19880200	Weak transcription	Aorta	Aorta
15	chr17:19851600-19858600	Weak transcription	NHEK	skin
16	chr17:19851600-19859200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr17:19851600-19859200	Weak transcription	HSMM	muscle
18	chr17:19851600-19859800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr17:19851600-19859800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr17:19851600-19871600	Weak transcription	Colonic Mucosa	Colon
21	chr17:19851800-19856000	Weak transcription	Fetal Lung	lung
22	chr17:19851800-19859200	Weak transcription	Osteobl	bone
23	chr17:19852000-19855800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:19852000-19856800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:19852000-19857000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr17:19852000-19857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:19852000-19857200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr17:19852000-19861200	Weak transcription	NHLF	lung
29	chr17:19852000-19871000	Weak transcription	Small Intestine	intestine
30	chr17:19852200-19855000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr17:19852200-19855400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:19852200-19855400	Weak transcription	Fetal Intestine Small	intestine
33	chr17:19852200-19855600	Weak transcription	Pancreas	Pancrea
34	chr17:19852200-19856800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr17:19852200-19856800	Weak transcription	Adipose Nuclei	Adipose
36	chr17:19852200-19856800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr17:19852200-19856800	Weak transcription	Placenta	Placenta
38	chr17:19852200-19857000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:19852200-19857000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr17:19852200-19857000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr17:19852200-19857000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr17:19852200-19857000	Weak transcription	Fetal Muscle Leg	muscle
43	chr17:19852200-19857000	Weak transcription	Lung	lung
44	chr17:19852200-19857000	Weak transcription	Thymus	Thymus
45	chr17:19852200-19857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr17:19852200-19857200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr17:19852200-19858600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:19852200-19858800	Weak transcription	Liver	Liver
49	chr17:19852200-19859000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr17:19852200-19859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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