Variant report

Variant	rs11638
Chromosome Location	chr10:96371928-96371929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1018602	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10786168	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10786169	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10786170	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882460	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs10882463	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs10882469	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10882470	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs10882471	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882473	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882474	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10882477	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10882481	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10882486	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11187939	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs11187944	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs11187948	0.91[MEX][hapmap];0.80[TSI][hapmap]
rs11187952	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11187960	0.83[JPT][hapmap]
rs11187972	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11187980	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[ASN][1000 genomes]
rs11187996	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11187998	0.80[JPT][hapmap]
rs11188009	1.00[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11188012	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188017	0.81[EUR][1000 genomes]
rs11188019	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188026	0.81[EUR][1000 genomes]
rs11188030	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11188038	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11188039	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11188040	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11188041	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11527881	0.84[ASN][1000 genomes]
rs11592354	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12218213	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs12218216	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs12219906	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs12220588	0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12221475	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12570013	0.85[EUR][1000 genomes]
rs12572040	0.83[EUR][1000 genomes]
rs12573638	0.80[JPT][hapmap]
rs1326839	0.92[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1334595	0.83[JPT][hapmap]
rs1359262	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1359263	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1409655	0.83[JPT][hapmap]
rs1854035	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1886272	0.86[ASN][1000 genomes]
rs1889486	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs1931757	1.00[JPT][hapmap]
rs1969815	0.85[CEU][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs1977288	0.83[JPT][hapmap]
rs1977291	1.00[JPT][hapmap]
rs1980741	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2095380	0.84[ASN][1000 genomes]
rs2148553	0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2274096	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2274417	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2281791	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2860821	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2860840	0.83[JPT][hapmap]
rs34814196	0.80[EUR][1000 genomes]
rs3740358	1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3758522	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3758523	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3781262	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4351744	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[ASN][1000 genomes]
rs4421688	0.81[EUR][1000 genomes]
rs4918401	0.80[EUR][1000 genomes]
rs4918402	1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4918404	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4918409	0.85[CEU][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4918411	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4918412	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4918417	0.80[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4918418	0.85[EUR][1000 genomes]
rs4918419	0.85[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs517784	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs6583942	0.83[JPT][hapmap]
rs6583943	0.85[ASN][1000 genomes]
rs6583944	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs6583945	0.81[EUR][1000 genomes]
rs6583946	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68046102	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs701885	1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7068337	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7078236	0.85[ASN][1000 genomes]
rs7078478	1.00[JPT][hapmap]
rs7078811	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7079934	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7083898	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7092129	0.83[JPT][hapmap]
rs7100415	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7906843	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7906968	0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7913343	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs7921721	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[ASN][1000 genomes]
rs912466	0.80[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs955694	0.80[JPT][hapmap]

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
rs11638	HELLS	cis	cerebellum	SCAN
rs11638	KIF11	cis	cerebellum	SCAN
rs11638	FGFBP3	cis	cerebellum	SCAN
rs11638	C19orf22	trans	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96306600-96379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:96306800-96373000	Weak transcription	Primary T cells from cord blood	blood
3	chr10:96307000-96375000	Weak transcription	Osteobl	bone
4	chr10:96307600-96373200	Weak transcription	Brain Germinal Matrix	brain
5	chr10:96307800-96373000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr10:96308000-96373200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:96309600-96372800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr10:96309600-96377000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr10:96312800-96372200	Strong transcription	Dnd41	blood
10	chr10:96314200-96373400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:96316000-96374000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr10:96316200-96373000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr10:96317000-96372600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr10:96324000-96376600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr10:96325800-96376000	Weak transcription	NHLF	lung
16	chr10:96331000-96377400	Weak transcription	Placenta	Placenta
17	chr10:96338800-96372000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:96345600-96372400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:96346600-96372600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr10:96354800-96376600	Weak transcription	Fetal Intestine Large	intestine
21	chr10:96355000-96375600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:96357000-96376200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr10:96357800-96372400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr10:96358400-96377200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr10:96359200-96373200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr10:96359200-96382000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr10:96360000-96373800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:96360400-96372400	Strong transcription	A549	lung
29	chr10:96361800-96372600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr10:96363200-96373200	Weak transcription	Fetal Muscle Leg	muscle
31	chr10:96363200-96376200	Weak transcription	HSMM	muscle
32	chr10:96363400-96374400	Weak transcription	NH-A	brain
33	chr10:96365200-96374200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr10:96365800-96372000	Weak transcription	Fetal Intestine Small	intestine
35	chr10:96366200-96376800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr10:96366400-96374000	Weak transcription	Fetal Stomach	stomach
37	chr10:96369200-96372000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr10:96369600-96374000	Weak transcription	GM12878-XiMat	blood
39	chr10:96369800-96375800	Weak transcription	Thymus	Thymus
40	chr10:96369800-96377200	Weak transcription	HMEC	breast
41	chr10:96370000-96373200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr10:96370000-96373600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr10:96370000-96374000	Weak transcription	Fetal Kidney	kidney
44	chr10:96370000-96377000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr10:96370000-96377000	Weak transcription	Hela-S3	cervix
46	chr10:96370000-96377200	Weak transcription	Fetal Lung	lung
47	chr10:96370000-96382800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr10:96370200-96382000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr10:96370400-96376200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr10:96370600-96382000	Weak transcription	H9 Cell Line	embryonic stem cell

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