Variant report

Variant	rs10217692
Chromosome Location	chr9:102710431-102710432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:102709867..102712687-chr9:102724069..102726821,2	K562	blood:
2	chr9:102580742..102583442-chr9:102708688..102711599,3	K562	blood:
3	chr9:102704572..102707723-chr9:102708233..102710529,3	K562	blood:
4	chr9:102705636..102707723-chr9:102708233..102710529,2	K562	blood:
5	chr9:102710112..102712767-chr9:102716660..102718329,2	K562	blood:
6	chr9:102710217..102711874-chr9:102712865..102715087,2	K562	blood:
7	chr9:102709867..102712687-chr9:102723477..102726821,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000237461	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10116142	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs10117638	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10117828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118565	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10120103	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs10121880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122128	0.93[ASN][1000 genomes]
rs10123261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124366	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10125981	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10217337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739791	0.93[ASN][1000 genomes]
rs10739792	0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs10739793	0.93[ASN][1000 genomes]
rs10739794	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10760698	0.92[ASN][1000 genomes]
rs10760699	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760700	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760705	0.92[ASN][1000 genomes]
rs10760706	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819705	0.92[ASN][1000 genomes]
rs10819706	0.93[ASN][1000 genomes]
rs10819707	0.93[ASN][1000 genomes]
rs10819711	0.93[ASN][1000 genomes]
rs10819712	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10988919	0.93[ASN][1000 genomes]
rs10988920	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10988945	0.87[YRI][hapmap]
rs10988973	0.82[YRI][hapmap]
rs12352899	0.93[ASN][1000 genomes]
rs1342147	0.82[YRI][hapmap]
rs1361668	0.82[YRI][hapmap]
rs1539297	0.82[YRI][hapmap]
rs16918878	0.88[JPT][hapmap]
rs1830454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881751	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1962051	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1969577	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1997367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031035	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2416937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416938	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs2416940	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416941	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416942	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2698999	0.87[YRI][hapmap]
rs2795575	0.87[YRI][hapmap]
rs2900224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739794	0.93[ASN][1000 genomes]
rs3983846	0.92[ASN][1000 genomes]
rs4282626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs4517187	0.82[YRI][hapmap]
rs4585797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742777	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478987	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478988	0.92[ASN][1000 genomes]
rs6478990	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022208	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7022999	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027813	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7030388	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7038506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853264	0.93[ASN][1000 genomes]
rs846759	0.82[YRI][hapmap]
rs9299335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9556	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1050510	chr9:102684318-102748658	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10217692	C9orf30	cis	cerebellum	SCAN
rs10217692	STX17	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102669800-102729800	Weak transcription	Small Intestine	intestine
2	chr9:102671200-102719200	Weak transcription	Fetal Heart	heart
3	chr9:102680000-102710800	Weak transcription	HUVEC	blood vessel
4	chr9:102680400-102724800	Weak transcription	HSMM	muscle
5	chr9:102682600-102751400	Weak transcription	NH-A	brain
6	chr9:102684400-102720600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:102685000-102731600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr9:102685200-102730200	Weak transcription	NHLF	lung
9	chr9:102686200-102730000	Weak transcription	Colonic Mucosa	Colon
10	chr9:102686400-102712800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:102686400-102713000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr9:102686400-102723400	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:102686400-102750800	Weak transcription	Esophagus	oesophagus
14	chr9:102686600-102713400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:102686600-102730800	Weak transcription	Ovary	ovary
16	chr9:102686600-102750800	Weak transcription	Gastric	stomach
17	chr9:102686800-102722800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr9:102687800-102722200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr9:102688200-102713400	Weak transcription	Dnd41	blood
20	chr9:102688400-102710800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:102689400-102713400	Weak transcription	Left Ventricle	heart
22	chr9:102689400-102713400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:102692800-102713400	Weak transcription	Fetal Thymus	thymus
24	chr9:102693000-102723000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:102694000-102713400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr9:102694000-102721600	Weak transcription	Fetal Stomach	stomach
27	chr9:102698400-102728600	Weak transcription	HMEC	breast
28	chr9:102698400-102728800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:102698600-102713600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:102699600-102713000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr9:102699600-102713400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:102699800-102711000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:102699800-102713000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:102699800-102713200	Weak transcription	Primary T cells from cord blood	blood
35	chr9:102699800-102713200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:102699800-102713400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr9:102699800-102713400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr9:102699800-102713400	Weak transcription	Liver	Liver
39	chr9:102699800-102713400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr9:102699800-102713400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:102699800-102713400	Weak transcription	Fetal Intestine Large	intestine
42	chr9:102699800-102722000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:102699800-102739800	Weak transcription	K562	blood
44	chr9:102699800-102765800	Weak transcription	Psoas Muscle	Psoas
45	chr9:102700000-102728600	Weak transcription	A549	lung
46	chr9:102700200-102713200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:102700200-102713400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:102700400-102713800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:102700600-102713400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr9:102700600-102713400	Weak transcription	Fetal Muscle Leg	muscle

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