Variant report

Variant	rs17396860
Chromosome Location	chr9:98766291-98766292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98753369..98756091-chr9:98765183..98768443,3	K562	blood:
2	chr9:98758966..98761197-chr9:98765461..98768218,3	K562	blood:
3	chr9:98758267..98760888-chr9:98765461..98767832,3	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10512243	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512244	0.85[GIH][hapmap];0.93[TSI][hapmap]
rs1410297	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1434729	0.81[AMR][1000 genomes]
rs16910291	0.83[CEU][hapmap];0.90[AMR][1000 genomes]
rs16910302	0.83[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes]
rs16910370	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs16910376	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16910382	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16910396	0.85[GIH][hapmap];0.87[TSI][hapmap]
rs17303045	0.83[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes]
rs17304942	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17305138	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]
rs17305329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305917	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17394582	0.83[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs17394881	0.98[AMR][1000 genomes]
rs17396240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[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]
rs17396338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396553	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]
rs1972802	0.86[AMR][1000 genomes]
rs2026643	0.85[YRI][hapmap]
rs2149099	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2149100	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2176026	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs3802439	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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144585	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs55645821	0.84[EUR][1000 genomes]
rs55699149	0.90[AMR][1000 genomes]
rs55746108	0.90[AMR][1000 genomes]
rs55787215	0.87[EUR][1000 genomes]
rs55810950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923424	0.90[AMR][1000 genomes]
rs55962207	0.83[AMR][1000 genomes]
rs55983886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56016781	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56108623	0.98[AMR][1000 genomes]
rs56162045	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56217203	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56225283	0.84[EUR][1000 genomes]
rs56379566	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56678652	1.00[AMR][1000 genomes]
rs62559011	0.90[AMR][1000 genomes]
rs62559012	0.90[AMR][1000 genomes]
rs62559013	0.90[AMR][1000 genomes]
rs62559025	0.90[AMR][1000 genomes]
rs62559027	0.90[AMR][1000 genomes]
rs62559029	0.93[AMR][1000 genomes]
rs62559030	0.93[AMR][1000 genomes]
rs62559031	0.93[AMR][1000 genomes]
rs62559053	0.98[AMR][1000 genomes]
rs62559054	1.00[AMR][1000 genomes]
rs62559055	1.00[AMR][1000 genomes]
rs62559057	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62559058	0.98[AMR][1000 genomes]
rs62559059	1.00[AMR][1000 genomes]
rs62559760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62559762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559769	0.87[EUR][1000 genomes]
rs62559794	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62559796	0.84[EUR][1000 genomes]
rs62562960	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62562961	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62562963	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62562966	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562967	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562970	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562979	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562980	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562981	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562982	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562985	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562989	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562992	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73532684	0.82[AMR][1000 genomes]
rs7864473	0.82[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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
2	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
3	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:98719400-98767200	Weak transcription	Right Ventricle	heart
5	chr9:98719400-98771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:98719600-98766800	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:98726400-98767800	Weak transcription	Gastric	stomach
8	chr9:98734600-98767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:98734600-98782400	Weak transcription	NHEK	skin
10	chr9:98735400-98778400	Weak transcription	Hela-S3	cervix
11	chr9:98735800-98766600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:98735800-98770600	Weak transcription	K562	blood
13	chr9:98735800-98771200	Weak transcription	HepG2	liver
14	chr9:98736600-98778800	Weak transcription	Fetal Brain Male	brain
15	chr9:98737000-98766800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:98741800-98778600	Weak transcription	NH-A	brain
17	chr9:98744600-98768000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:98744800-98766800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr9:98744800-98770800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr9:98744800-98771000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr9:98745000-98766800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr9:98747800-98782800	Weak transcription	Fetal Kidney	kidney
23	chr9:98748000-98782600	Weak transcription	HMEC	breast
24	chr9:98748200-98771000	Weak transcription	Fetal Heart	heart
25	chr9:98748400-98766600	Weak transcription	HSMM	muscle
26	chr9:98748400-98767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:98748400-98767800	Weak transcription	NHLF	lung
28	chr9:98748400-98768400	Weak transcription	HSMMtube	muscle
29	chr9:98748400-98770600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:98748400-98782800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:98748600-98766800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:98748600-98781200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr9:98748800-98766600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:98748800-98766800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:98749400-98770800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:98749600-98770200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:98750000-98766600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr9:98750200-98766600	Weak transcription	Dnd41	blood
39	chr9:98750200-98766800	Weak transcription	Fetal Thymus	thymus
40	chr9:98750400-98768200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr9:98750400-98768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:98750400-98771400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:98750400-98771400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:98750800-98771000	Weak transcription	A549	lung
45	chr9:98751600-98767800	Weak transcription	Colonic Mucosa	Colon
46	chr9:98751600-98772600	Weak transcription	Small Intestine	intestine
47	chr9:98751800-98767800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:98752200-98766600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:98752200-98766800	Weak transcription	NHDF-Ad	bronchial
50	chr9:98752400-98768600	Weak transcription	Osteobl	bone

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