Variant report

Variant	rs2025445
Chromosome Location	chr10:96370263-96370264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1042192	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs1042194	0.81[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs1048196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10509676	0.82[CHB][hapmap];0.86[YRI][hapmap]
rs1065027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11187998	0.83[LWK][hapmap]
rs11594492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11595478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12219906	0.81[LWK][hapmap]
rs12570771	0.84[AFR][1000 genomes]
rs12571306	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12571421	0.82[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs12571659	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12767583	0.87[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs12768009	0.82[CHD][hapmap];0.84[LWK][hapmap];0.86[YRI][hapmap]
rs12769392	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12770064	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs12772672	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs12773342	0.82[CHB][hapmap];0.86[YRI][hapmap]
rs12774450	0.88[AFR][1000 genomes]
rs12774901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12778026	0.81[CHB][hapmap]
rs12778216	0.83[AFR][1000 genomes]
rs12783717	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12784245	0.85[AFR][1000 genomes]
rs1326832	0.82[CHB][hapmap]
rs1926711	0.80[GIH][hapmap]
rs1926712	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2031322	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2151953	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2281890	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2281891	0.86[ASW][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs2296680	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap]
rs2860837	0.84[AFR][1000 genomes]
rs2860838	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs34151925	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35134124	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35172334	0.83[AFR][1000 genomes]
rs35390752	0.82[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.81[LWK][hapmap]
rs35751085	0.80[AFR][1000 genomes]
rs35805353	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3818504	0.85[AFR][1000 genomes]
rs4244285	0.82[CHB][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs4532967	0.80[AFR][1000 genomes]
rs4641393	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs4986894	0.82[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs58335703	0.83[AFR][1000 genomes]
rs6583954	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap]
rs7085890	0.82[CHB][hapmap]
rs7089349	0.87[AFR][1000 genomes]
rs7100783	0.82[CHB][hapmap];0.86[YRI][hapmap]
rs71482318	0.80[AFR][1000 genomes]
rs717238	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap]
rs7893282	0.85[AFR][1000 genomes]
rs7900135	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs932809	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs9783239	0.83[AFR][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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv517681	chr10:96343228-96387079	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2025445	ZFYVE27	cis	parietal	SCAN
rs2025445	CYP2C19	cis	Esophagus Mucosa	GTEx
rs2025445	GOLGA7B	cis	parietal	SCAN
rs2025445	HELLS	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96306400-96370400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:96306400-96370600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr10:96306400-96371000	Weak transcription	Ovary	ovary
4	chr10:96306600-96379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:96306800-96373000	Weak transcription	Primary T cells from cord blood	blood
6	chr10:96307000-96375000	Weak transcription	Osteobl	bone
7	chr10:96307200-96371200	Weak transcription	Fetal Brain Male	brain
8	chr10:96307600-96373200	Weak transcription	Brain Germinal Matrix	brain
9	chr10:96307800-96373000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:96308000-96373200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:96309600-96372800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:96309600-96377000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr10:96312800-96372200	Strong transcription	Dnd41	blood
14	chr10:96314200-96373400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr10:96316000-96371400	Weak transcription	Fetal Brain Female	brain
16	chr10:96316000-96374000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr10:96316200-96373000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr10:96317000-96372600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr10:96324000-96376600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:96325800-96376000	Weak transcription	NHLF	lung
21	chr10:96331000-96377400	Weak transcription	Placenta	Placenta
22	chr10:96338800-96372000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:96345400-96371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr10:96345600-96372400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr10:96346600-96372600	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr10:96348600-96371400	Weak transcription	NHEK	skin
27	chr10:96349200-96371000	Weak transcription	Primary B cells from cord blood	blood
28	chr10:96350600-96371800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr10:96351400-96371000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:96354800-96376600	Weak transcription	Fetal Intestine Large	intestine
31	chr10:96355000-96375600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:96357000-96376200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:96357800-96372400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr10:96358200-96371600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr10:96358400-96377200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr10:96359200-96373200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr10:96359200-96382000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr10:96360000-96371400	Weak transcription	HepG2	liver
39	chr10:96360000-96373800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr10:96360400-96372400	Strong transcription	A549	lung
41	chr10:96361800-96372600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr10:96362200-96371000	Weak transcription	NHDF-Ad	bronchial
43	chr10:96362400-96371200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:96363200-96371400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr10:96363200-96373200	Weak transcription	Fetal Muscle Leg	muscle
46	chr10:96363200-96376200	Weak transcription	HSMM	muscle
47	chr10:96363400-96374400	Weak transcription	NH-A	brain
48	chr10:96365200-96374200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr10:96365800-96372000	Weak transcription	Fetal Intestine Small	intestine
50	chr10:96366000-96370600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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