Variant report

Variant	rs1417731
Chromosome Location	chr10:93635541-93635542
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	chr10:93630115..93633090-chr10:93633153..93635901,2	K562	blood:
2	chr10:93628714..93630767-chr10:93634147..93636054,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10509635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10509638	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10509639	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11592379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11592537	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11593642	0.81[ASN][1000 genomes]
rs11593805	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11594021	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11594359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11595800	0.83[AMR][1000 genomes]
rs11597639	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11598220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11598809	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11599407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1417730	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1538833	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1539042	0.84[JPT][hapmap]
rs17107004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs17107010	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17107019	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17107075	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17107084	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17107090	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17107109	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17107140	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1772189	0.84[JPT][hapmap]
rs2000139	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2050914	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2096080	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2096081	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2105296	0.83[AMR][1000 genomes]
rs2185596	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2275646	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421693	0.81[ASN][1000 genomes]
rs2421698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3758501	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3802650	0.84[JPT][hapmap]
rs3808930	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3949338	0.81[ASN][1000 genomes]
rs41286940	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4373831	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs68185109	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7067554	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7067679	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7067694	0.81[AMR][1000 genomes]
rs7067882	0.81[AMR][1000 genomes]
rs7068403	0.81[AMR][1000 genomes]
rs7072165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7076618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7083631	0.81[AMR][1000 genomes]
rs7091015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs7091147	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7093641	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7097415	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73325905	0.81[AMR][1000 genomes]
rs73325918	0.83[AMR][1000 genomes]
rs73327861	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73327866	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7894188	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7895548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7906154	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7920215	0.90[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv7491	chr10:93626192-93671694	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv511445	chr10:93627158-93635541	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3531002	chr10:93631372-93636470	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3442817	chr10:93631922-93635720	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3387055	chr10:93632397-93635845	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3398993	chr10:93632622-93635570	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1819110	chr10:93634155-93643195	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv1842657	chr10:93634155-93668663	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1417731	DNAH2	trans	cerebellum	SCAN
rs1417731	TCTN3	cis	parietal	SCAN
rs1417731	CYP26A1	cis	cerebellum	SCAN
rs1417731	HELLS	cis	cerebellum	SCAN
rs1417731	CYP2C9	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93608800-93639200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:93608800-93643400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:93618400-93639400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr10:93622600-93639000	Weak transcription	Brain Germinal Matrix	brain
5	chr10:93622800-93639200	Weak transcription	Brain Angular Gyrus	brain
6	chr10:93624200-93639200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:93625800-93639000	Weak transcription	Fetal Brain Female	brain
8	chr10:93626200-93639600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr10:93626200-93643000	Weak transcription	HSMMtube	muscle
10	chr10:93627600-93639000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:93627600-93639600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:93627800-93639000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:93629600-93638800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:93629600-93639000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr10:93629600-93639200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:93632800-93639200	Weak transcription	Placenta	Placenta
17	chr10:93634800-93639000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr10:93634800-93639000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr10:93634800-93639000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:93635000-93643200	Weak transcription	Right Atrium	heart
21	chr10:93635200-93639200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:93635400-93636000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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