Variant report

Variant	rs17619360
Chromosome Location	chr6:56996466-56996467
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56953178..56955896-chr6:56996170..56998896,2	K562	blood:
2	chr6:56994508..56996955-chr6:57008471..57010355,2	K562	blood:
3	chr6:56994688..56997682-chr6:56999220..57001333,3	K562	blood:
4	chr6:56993514..56996955-chr6:57008261..57010355,3	K562	blood:
5	chr6:56995928..56997999-chr6:57012848..57014485,2	K562	blood:
6	chr6:56990747..56993743-chr6:56994330..56996641,2	K562	blood:
7	chr6:56956880..56959339-chr6:56996138..56998446,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112200	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1020550	0.90[ASN][1000 genomes]
rs1044670	0.88[CEU][hapmap]
rs10456192	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10484410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11398	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12190575	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192222	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194288	0.90[ASN][1000 genomes]
rs12194407	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198801	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201039	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211901	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12214119	0.91[EUR][1000 genomes]
rs12214882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1547226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16888392	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3800018	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs3800023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800025	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3957366	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs3996934	0.90[ASN][1000 genomes]
rs3996935	0.90[ASN][1000 genomes]
rs3996936	0.90[ASN][1000 genomes]
rs4523090	0.90[ASN][1000 genomes]
rs4631287	0.90[ASN][1000 genomes]
rs6459178	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];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6918222	0.82[EUR][1000 genomes]
rs6936506	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72868608	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73463742	0.80[ASN][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7753547	0.90[ASN][1000 genomes]
rs7756421	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];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7771115	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];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349841	0.85[ASN][1000 genomes]
rs9396247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9396256	0.90[ASN][1000 genomes]
rs986245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17619360	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs17619360	BEND6	cis	Muscle Skeletal	GTEx
rs17619360	RAB23	cis	lymphoblastoid	seeQTL
rs17619360	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs17619360	BEND6	cis	parietal	SCAN
rs17619360	BEND6	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56966600-57012400	Weak transcription	Spleen	Spleen
2	chr6:56966800-57018000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:56968200-57036400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:56968400-57000800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:56968600-56998200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:56968600-57002200	Weak transcription	Thymus	Thymus
7	chr6:56968600-57006600	Weak transcription	Brain Angular Gyrus	brain
8	chr6:56968600-57018400	Weak transcription	Psoas Muscle	Psoas
9	chr6:56969200-56997800	Weak transcription	Fetal Lung	lung
10	chr6:56969400-56997400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:56969400-56997800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:56969600-56997600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:56969600-56999000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:56970200-57007600	Weak transcription	Fetal Kidney	kidney
15	chr6:56973600-56997000	Weak transcription	NHEK	skin
16	chr6:56973800-56998400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:56974000-57001000	Weak transcription	NH-A	brain
18	chr6:56974000-57012400	Weak transcription	HUVEC	blood vessel
19	chr6:56974200-57012000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:56974400-56999600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:56975000-56997800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:56975000-57006400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:56975400-57006800	Weak transcription	NHLF	lung
24	chr6:56982400-56997800	Weak transcription	Osteobl	bone
25	chr6:56984000-56998400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:56985600-56998000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:56985600-57036800	Weak transcription	Pancreas	Pancrea
28	chr6:56986000-56998400	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:56986200-56998600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:56986400-57012000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:56987800-56997800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:56988000-56997800	Weak transcription	Fetal Thymus	thymus
33	chr6:56988000-56998400	Weak transcription	Aorta	Aorta
34	chr6:56988000-56998600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:56988000-57009000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:56988200-56997800	Weak transcription	Dnd41	blood
37	chr6:56988200-56998600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:56988200-56999600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:56988200-57009400	Weak transcription	Fetal Intestine Small	intestine
40	chr6:56988400-56997200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:56988400-56997400	Weak transcription	Left Ventricle	heart
42	chr6:56988400-56997800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:56988400-56998000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr6:56988400-56998200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:56988400-56998800	Weak transcription	Fetal Brain Female	brain
46	chr6:56990200-56997200	Weak transcription	GM12878-XiMat	blood
47	chr6:56991600-57036600	Weak transcription	Small Intestine	intestine
48	chr6:56992000-56998600	Weak transcription	Brain Substantia Nigra	brain
49	chr6:56992200-57006600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:56992600-57000000	Strong transcription	Primary B cells from cord blood	blood

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