Variant report

Variant	rs9396259
Chromosome Location	chr6:56981688-56981689
allele	A/C
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:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:56977388..56979251-chr6:56980125..56981936,2	K562	blood:
2	chr6:56975731..56978915-chr6:56980133..56983784,4	K562	blood:
3	chr6:56978877..56981923-chr6:56988511..56992280,3	K562	blood:
4	chr6:56967474..56971022-chr6:56981374..56983597,3	K562	blood:
5	chr6:56980722..56982441-chr6:56985214..56987873,2	K562	blood:
6	chr6:56980361..56982548-chr6:57043323..57045431,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB23-2	chr6:56981638-56981719	ENSG00000226803.3
2	lnc-RAB23-2	chr6:56981638-56981719	ENSG00000226803.3

No data

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1157713	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190416	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190434	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192711	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12210597	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12211611	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1901382	0.81[EUR][1000 genomes]
rs2100305	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2273921	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734738	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778515	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800019	0.93[ASN][1000 genomes]
rs3996929	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3996933	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3996937	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4715646	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6459180	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6913707	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6926980	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6928715	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6929783	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6936472	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743855	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7744316	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7744824	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7753537	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753927	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7763570	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8180538	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349843	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367704	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367708	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370564	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370565	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382689	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952647	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885757	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9396259	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs9396259	RAB23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56966600-56987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:56966600-56987600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:56966600-57012400	Weak transcription	Spleen	Spleen
4	chr6:56966800-56987600	Weak transcription	Fetal Intestine Small	intestine
5	chr6:56966800-57018000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:56967000-56983400	Weak transcription	Fetal Stomach	stomach
7	chr6:56967200-56992200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:56967800-56992400	Weak transcription	A549	lung
9	chr6:56967800-56995400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:56967800-56995800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:56968000-56987800	Weak transcription	Aorta	Aorta
12	chr6:56968000-56993400	Weak transcription	Liver	Liver
13	chr6:56968000-56993600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:56968200-56986400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:56968200-56987000	Weak transcription	Fetal Intestine Large	intestine
16	chr6:56968200-57036400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:56968400-56993200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:56968400-57000800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:56968600-56987800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:56968600-56987800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:56968600-56998200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:56968600-57002200	Weak transcription	Thymus	Thymus
23	chr6:56968600-57006600	Weak transcription	Brain Angular Gyrus	brain
24	chr6:56968600-57018400	Weak transcription	Psoas Muscle	Psoas
25	chr6:56969000-56986600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:56969200-56986600	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:56969200-56987200	Weak transcription	Adipose Nuclei	Adipose
28	chr6:56969200-56987600	Weak transcription	Left Ventricle	heart
29	chr6:56969200-56987800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:56969200-56995400	Weak transcription	Brain Anterior Caudate	brain
31	chr6:56969200-56997800	Weak transcription	Fetal Lung	lung
32	chr6:56969400-56987800	Weak transcription	Fetal Thymus	thymus
33	chr6:56969400-56993600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:56969400-56997400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:56969400-56997800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:56969600-56983400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:56969600-56987600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr6:56969600-56990400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:56969600-56997600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:56969600-56999000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:56969800-56981800	Weak transcription	Osteobl	bone
42	chr6:56969800-56987800	Weak transcription	Fetal Brain Female	brain
43	chr6:56970200-56987400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:56970200-57007600	Weak transcription	Fetal Kidney	kidney
45	chr6:56970600-56993000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:56971000-56993200	Weak transcription	Placenta	Placenta
47	chr6:56971200-56986600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:56972200-56987600	Weak transcription	Dnd41	blood
49	chr6:56972200-56994000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:56973400-56993600	Weak transcription	HMEC	breast

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