Variant report

Variant	rs16909005
Chromosome Location	chr9:96065578-96065579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:96065540-96065690	HEK293	kidney:	n/a	n/a
2	CTCF	chr9:96065440-96065590	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr9:96064944-96066056	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:96065384-96065753	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:96065418-96065578	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr9:96065520-96065670	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96062588..96064123-chr9:96065486..96067429,2	MCF-7	breast:
2	chr9:96064647..96066997-chr9:96073946..96076546,2	MCF-7	breast:
3	chr9:95960515..95962748-chr9:96063970..96065844,2	MCF-7	breast:
4	chr9:95921857..95922911-chr9:96064779..96065588,5	MCF-7	breast:
5	chr9:95895149..95897720-chr9:96064808..96066436,2	MCF-7	breast:
6	chr9:95921936..95922821-chr9:96064640..96065645,10	MCF-7	breast:
7	chr9:96065577..96067663-chr9:96072266..96075048,2	K562	blood:
8	chr9:96063114..96067393-chr9:96338286..96340131,3	MCF-7	breast:
9	chr9:95953204..95955785-chr9:96063844..96066566,2	MCF-7	breast:

No data

Variant related genes	Relation type
WNK2	TF binding region
ENSG00000131669	Chromatin interaction
ENSG00000197724	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10122466	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10512233	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10761208	1.00[MEX][hapmap]
rs1539670	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16909000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16909016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16936750	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16936752	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1891971	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1891972	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1891973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1936403	0.83[AMR][1000 genomes]
rs1970622	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4744197	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs4744202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4744205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs55643343	0.90[EUR][1000 genomes]
rs55692827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55706397	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55795421	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56300939	0.90[EUR][1000 genomes]
rs59491442	0.89[EUR][1000 genomes]
rs6479467	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7029968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72743431	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72743433	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743435	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743442	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72743443	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72743444	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743445	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743446	0.89[EUR][1000 genomes]
rs72743448	0.89[EUR][1000 genomes]
rs72743449	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72743451	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7859604	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7859628	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7871272	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.83[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	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96033000-96067200	Weak transcription	Brain Angular Gyrus	brain
2	chr9:96033400-96067000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:96051400-96067800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:96052200-96066600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:96055600-96080200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:96056400-96079800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:96056800-96067400	Weak transcription	Brain Anterior Caudate	brain
10	chr9:96059600-96067000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr9:96060000-96066200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:96061000-96065800	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:96061000-96072200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:96061200-96067400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:96061400-96075000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:96061600-96066800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:96061600-96066800	Weak transcription	Left Ventricle	heart
18	chr9:96061600-96067000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:96061600-96070200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:96061600-96079000	Weak transcription	Gastric	stomach
21	chr9:96061800-96066200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:96062000-96066600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:96062400-96065600	Enhancers	HepG2	liver
24	chr9:96062600-96069200	Enhancers	Fetal Muscle Leg	muscle
25	chr9:96063000-96070200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:96063200-96066800	Weak transcription	Psoas Muscle	Psoas
27	chr9:96063200-96072200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:96063400-96067400	Weak transcription	Adipose Nuclei	Adipose
29	chr9:96063400-96069200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:96063600-96070600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:96063800-96066000	Weak transcription	Fetal Heart	heart
32	chr9:96063800-96067000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr9:96063800-96067400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:96063800-96088600	Weak transcription	Right Atrium	heart
35	chr9:96064000-96066000	Enhancers	Fetal Thymus	thymus
36	chr9:96064000-96066400	Weak transcription	Right Ventricle	heart
37	chr9:96064200-96065800	Weak transcription	Fetal Brain Female	brain
38	chr9:96064600-96065600	Weak transcription	Brain Germinal Matrix	brain
39	chr9:96064800-96065600	Enhancers	Fetal Muscle Trunk	muscle
40	chr9:96064800-96067200	Genic enhancers	Pancreas	Pancrea
41	chr9:96064800-96070200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr9:96065000-96065600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr9:96065000-96066600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:96065000-96067600	Enhancers	Fetal Brain Male	brain
45	chr9:96065000-96067600	Weak transcription	Fetal Intestine Large	intestine
46	chr9:96065000-96079200	Weak transcription	Colonic Mucosa	Colon
47	chr9:96065200-96066600	Weak transcription	Fetal Stomach	stomach
48	chr9:96065200-96067200	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:96065200-96067400	Weak transcription	Stomach Mucosa	stomach
50	chr9:96065200-96080000	Weak transcription	Spleen	Spleen

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