Variant report

Variant	rs17110519
Chromosome Location	chr1:84968749-84968750
allele	G/T
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	USF1	chr1:84968571-84968926	SK-N-SH	brain:	n/a	chr1:84968754-84968775 chr1:84968761-84968770 chr1:84968760-84968769 chr1:84968759-84968768 chr1:84968760-84968769 chr1:84968758-84968771
2	POLR2A	chr1:84957385-84973725	K562	blood:	n/a	n/a
3	USF1	chr1:84968634-84968941	SK-N-SH_RA	brain:	n/a	chr1:84968754-84968775 chr1:84968761-84968770 chr1:84968760-84968769 chr1:84968759-84968768 chr1:84968760-84968769 chr1:84968758-84968771
4	POLR2A	chr1:84968600-84968953	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:84968320-84972670	HepG2	liver:	n/a	n/a
6	USF1	chr1:84968625-84968924	K562	blood:	n/a	chr1:84968754-84968775 chr1:84968761-84968770 chr1:84968760-84968769 chr1:84968759-84968768 chr1:84968760-84968769 chr1:84968758-84968771
7	POLR2A	chr1:84968524-84972839	PANC-1	pancreas:	n/a	n/a
8	USF1	chr1:84968590-84968844	SK-N-SH_RA	brain:	n/a	chr1:84968754-84968775 chr1:84968761-84968770 chr1:84968760-84968769 chr1:84968759-84968768 chr1:84968760-84968769 chr1:84968758-84968771
9	POLR2A	chr1:84968683-84972955	HepG2	liver:	n/a	n/a
10	USF2	chr1:84968642-84968828	GM12878	blood:	n/a	chr1:84968754-84968775 chr1:84968761-84968770 chr1:84968760-84968769 chr1:84968759-84968768 chr1:84968760-84968769 chr1:84968758-84968771

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
2	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:

Variant related genes	Relation type
SPATA1	TF binding region
ENSG00000117151	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11163971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11163972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11163980	0.81[CHB][hapmap]
rs11163981	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11163992	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1123981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1144276	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11578494	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11586006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12071149	0.81[CHB][hapmap]
rs12123381	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12124568	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12124731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128801	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs12136756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12137559	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12140555	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12143652	0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs12145405	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1246159	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1395416	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1395417	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1506707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17109982	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17110030	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1911159	0.81[CHB][hapmap]
rs2271620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292191	0.82[CHD][hapmap]
rs2292808	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659173	0.81[CHB][hapmap]
rs2794218	0.81[CHB][hapmap]
rs312395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs312397	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs3813605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3813607	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922538	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4906995	0.81[CHB][hapmap]
rs4907076	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907077	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907078	0.81[CHB][hapmap]
rs56212819	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57245302	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57442052	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6704211	0.81[CHB][hapmap]
rs74095416	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74095424	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74095432	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74095436	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7512922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513490	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7519606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535445	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7536988	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925740	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17110519	CTBS	cis	multi-tissue	Pritchard
rs17110519	SPATA1	cis	multi-tissue	Pritchard
rs17110519	SPATA1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
2	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:84947400-84969800	Weak transcription	Aorta	Aorta
5	chr1:84951200-84971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:84954800-84969200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:84955200-84968800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:84955200-84968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:84956000-84969400	Weak transcription	Pancreas	Pancrea
10	chr1:84956800-84969400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:84956800-84970400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:84958000-84968800	Weak transcription	Right Ventricle	heart
13	chr1:84958600-84969400	Weak transcription	Gastric	stomach
14	chr1:84958600-84970400	Weak transcription	Lung	lung
15	chr1:84960600-84968800	Weak transcription	Psoas Muscle	Psoas
16	chr1:84961400-84968800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:84963000-84968800	Weak transcription	Fetal Stomach	stomach
18	chr1:84963000-84969400	Weak transcription	Spleen	Spleen
19	chr1:84963000-84969600	Weak transcription	Colonic Mucosa	Colon
20	chr1:84963800-84969400	Weak transcription	A549	lung
21	chr1:84963800-84970200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:84963800-84970200	Weak transcription	Fetal Brain Male	brain
23	chr1:84963800-84970400	Weak transcription	Brain Angular Gyrus	brain
24	chr1:84964000-84968800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:84964000-84969400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:84964000-84969800	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:84964000-84969800	Weak transcription	Ovary	ovary
28	chr1:84964000-84970200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:84964600-84968800	Weak transcription	Fetal Kidney	kidney
30	chr1:84964600-84969600	Weak transcription	Brain Substantia Nigra	brain
31	chr1:84964800-84969000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:84964800-84969400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:84964800-84969400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:84965400-84968800	Weak transcription	Fetal Brain Female	brain
35	chr1:84965800-84968800	Genic enhancers	Dnd41	blood
36	chr1:84965800-84970400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:84966000-84969000	Enhancers	Fetal Heart	heart
38	chr1:84966000-84969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:84966000-84969600	Weak transcription	Thymus	Thymus
40	chr1:84966400-84969200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
41	chr1:84966600-84969000	Weak transcription	Fetal Lung	lung
42	chr1:84966800-84970400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr1:84967000-84968800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:84967000-84969400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:84967000-84969400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:84967000-84969600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr1:84967000-84970000	Weak transcription	Placenta	Placenta
48	chr1:84967200-84968800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:84967200-84968800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:84967200-84968800	Weak transcription	Small Intestine	intestine

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