Variant report

Variant	rs2317700
Chromosome Location	chr3:101143166-101143167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1019677	0.89[EUR][1000 genomes]
rs10936607	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936642	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10936664	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12491955	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12496260	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13087404	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13089177	0.80[ASN][1000 genomes]
rs13089552	0.85[ASN][1000 genomes]
rs13320918	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13322987	0.95[EUR][1000 genomes]
rs16843927	0.95[EUR][1000 genomes]
rs1918405	0.89[EUR][1000 genomes]
rs2141179	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2141180	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178036	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2250611	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317699	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317745	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317749	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317751	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433031	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553416	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553424	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2553427	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553430	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682383	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682384	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682386	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682390	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682391	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28460520	0.80[EUR][1000 genomes]
rs28565548	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34255148	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs348866	0.81[ASN][1000 genomes]
rs348869	0.82[ASN][1000 genomes]
rs3846091	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4287896	0.89[EUR][1000 genomes]
rs4456838	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4524254	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683899	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683900	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683917	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683918	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs473702	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497953	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs503734	0.88[ASN][1000 genomes]
rs508537	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs520558	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs533852	0.82[ASN][1000 genomes]
rs551442	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56075912	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62280667	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441602	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441608	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441610	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6771561	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6772703	0.94[EUR][1000 genomes]
rs6773536	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7628681	0.89[EUR][1000 genomes]
rs7631506	0.94[EUR][1000 genomes]
rs7636475	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9814991	0.91[EUR][1000 genomes]
rs9843186	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9856435	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9859077	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9870114	0.80[ASN][1000 genomes]
rs9874188	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2317700	SENP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101107200-101161200	Weak transcription	Aorta	Aorta
2	chr3:101111600-101145800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:101127400-101143200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:101128600-101146200	Weak transcription	Dnd41	blood
5	chr3:101129200-101160000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:101133400-101143200	Weak transcription	Pancreas	Pancrea
7	chr3:101133600-101160600	Weak transcription	K562	blood
8	chr3:101134600-101143200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:101134600-101143400	Weak transcription	Primary T cells from cord blood	blood
10	chr3:101134600-101143400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:101135000-101144200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:101136800-101144200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:101137200-101143600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:101141000-101185600	Weak transcription	Right Ventricle	heart
15	chr3:101141200-101143200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:101141200-101143400	Weak transcription	Left Ventricle	heart
17	chr3:101141200-101144200	Weak transcription	Primary B cells from cord blood	blood
18	chr3:101141200-101160000	Weak transcription	Gastric	stomach
19	chr3:101142200-101143600	ZNF genes & repeats	Fetal Intestine Small	intestine
20	chr3:101142200-101145000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr3:101142200-101146000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:101142200-101146200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr3:101142400-101143400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:101142400-101143600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:101142400-101143600	ZNF genes & repeats	Brain Germinal Matrix	brain
26	chr3:101142400-101143800	ZNF genes & repeats	Fetal Stomach	stomach
27	chr3:101142400-101144200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr3:101142400-101144400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:101142400-101146000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:101142400-101146400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:101142600-101143400	Enhancers	Esophagus	oesophagus
32	chr3:101142600-101143600	ZNF genes & repeats	Fetal Thymus	thymus
33	chr3:101142600-101143800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:101142600-101144600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr3:101143000-101143200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:101143000-101143600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:101143000-101143800	Genic enhancers	Spleen	Spleen

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