Variant report

Variant	rs203470
Chromosome Location	chr17:19858626-19858627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19849218..19850772-chr17:19856829..19859320,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11204419	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204420	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204421	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs119672	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1479129	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1638525	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166840	0.82[EUR][1000 genomes]
rs169412	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169414	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs175921	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs175922	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs191865	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203450	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203451	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203452	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203455	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203456	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203457	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203458	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203459	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203460	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203461	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203462	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203465	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203466	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203469	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203477	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203479	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203481	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203482	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2108978	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397969	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs427798	0.89[EUR][1000 genomes]
rs4479308	0.82[ASN][1000 genomes]
rs4925060	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56153261	0.86[ASN][1000 genomes]
rs6587206	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7222403	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8066150	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs850623	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860335	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9907752	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9914273	0.90[EUR][1000 genomes]
rs9914304	0.86[EUR][1000 genomes]
rs9916675	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[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
rs203470	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr17:19846800-19875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:19850600-19861000	Weak transcription	NH-A	brain
7	chr17:19850600-19861400	Weak transcription	Gastric	stomach
8	chr17:19850600-19861600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:19850600-19879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr17:19850600-19880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:19850600-19880200	Weak transcription	Aorta	Aorta
12	chr17:19851600-19859200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr17:19851600-19859200	Weak transcription	HSMM	muscle
14	chr17:19851600-19859800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:19851600-19859800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr17:19851600-19871600	Weak transcription	Colonic Mucosa	Colon
17	chr17:19851800-19859200	Weak transcription	Osteobl	bone
18	chr17:19852000-19861200	Weak transcription	NHLF	lung
19	chr17:19852000-19871000	Weak transcription	Small Intestine	intestine
20	chr17:19852200-19858800	Weak transcription	Liver	Liver
21	chr17:19852200-19859000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr17:19852200-19859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:19852200-19859400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr17:19852200-19861000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:19852200-19861000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr17:19852200-19861200	Weak transcription	Brain Hippocampus Middle	brain
27	chr17:19852200-19861200	Weak transcription	Brain Substantia Nigra	brain
28	chr17:19852200-19861200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr17:19852200-19861400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:19852200-19862200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:19852200-19865000	Weak transcription	Ovary	ovary
32	chr17:19852200-19866000	Weak transcription	Spleen	Spleen
33	chr17:19852200-19879400	Weak transcription	Esophagus	oesophagus
34	chr17:19852200-19879600	Weak transcription	Right Ventricle	heart
35	chr17:19852200-19880000	Weak transcription	Psoas Muscle	Psoas
36	chr17:19852400-19859200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr17:19852400-19859200	Weak transcription	Brain Angular Gyrus	brain
38	chr17:19852400-19859200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr17:19852400-19859200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr17:19852400-19859600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr17:19852400-19861000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr17:19852400-19861000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr17:19852400-19861000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr17:19852400-19861000	Weak transcription	HMEC	breast
45	chr17:19852400-19861200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr17:19852600-19859000	Weak transcription	Hela-S3	cervix
47	chr17:19852600-19859000	Weak transcription	HUVEC	blood vessel
48	chr17:19852600-19859400	Weak transcription	Colon Smooth Muscle	Colon
49	chr17:19852800-19869800	Weak transcription	Fetal Heart	heart
50	chr17:19853000-19859000	Weak transcription	Fetal Thymus	thymus

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