Variant report

Variant	rs16909000
Chromosome Location	chr9:96065179-96065180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr9:96064751-96065462	MCF-7	breast:	n/a	chr9:96064941-96064953 chr9:96065137-96065156
2	CTCF	chr9:96065040-96065190	A549	lung:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
3	CTCF	chr9:96065040-96065190	GM12871	blood:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
4	USF1	chr9:96065032-96065336	K562	blood:	n/a	chr9:96065174-96065185
5	CTCF	chr9:96065037-96065209	SK-N-SH_RA	brain:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
6	CTCF	chr9:96064721-96065359	MCF-7	breast:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
7	RAD21	chr9:96064889-96065305	SK-N-SH_RA	brain:	n/a	chr9:96064941-96064953 chr9:96065137-96065156
8	YY1	chr9:96064980-96065238	GM12878	blood:	n/a	n/a
9	CTCF	chr9:96065080-96065230	BJ	skin:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
10	CTCF	chr9:96065080-96065230	NHLF	lung:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
11	ZNF143	chr9:96065075-96065295	K562	blood:	n/a	n/a
12	BHLHE40	chr9:96065001-96065283	HepG2	liver:	n/a	n/a
13	USF1	chr9:96064958-96065278	ECC-1	luminal epithelium:	n/a	chr9:96065174-96065185
14	YY1	chr9:96064949-96065189	K562	blood:	n/a	n/a
15	USF1	chr9:96065076-96065237	HepG2	liver:	n/a	chr9:96065174-96065185
16	CTCF	chr9:96065060-96065210	K562	blood:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
17	RAD21	chr9:96064905-96065332	HepG2	liver:	n/a	chr9:96064941-96064953 chr9:96065137-96065156
18	CTCF	chr9:96064994-96065277	MCF-7	breast:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
19	CTCF	chr9:96064998-96065278	NHEK	skin:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
20	HDAC2	chr9:96064960-96065292	HepG2	liver:	n/a	n/a
21	STAT1	chr9:96064524-96065239	K562	blood:	n/a	chr9:96064794-96064803 chr9:96064789-96064809 chr9:96064795-96064804 chr9:96064810-96064824 chr9:96064798-96064821 chr9:96064812-96064821 chr9:96064813-96064822
22	CTCF	chr9:96065060-96065210	GM12864	blood:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
23	CTCF	chr9:96065031-96065290	Pancreas_OC	pancreas:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
24	CTCF	chr9:96065060-96065210	HMF	breast:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
25	CTCF	chr9:96065060-96065210	HA-sp	spinal cord:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
26	CTCF	chr9:96065100-96065250	AG09319	gingival:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
27	CTCF	chr9:96064816-96065280	HCT-116	colon:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
28	RAD21	chr9:96064876-96065271	ECC-1	luminal epithelium:	n/a	chr9:96064941-96064953 chr9:96065137-96065156
29	CTCF	chr9:96065080-96065230	HMEC	breast:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
30	CTCF	chr9:96065060-96065210	AG04449	skin:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
31	CTCF	chr9:96065080-96065230	GM12864	blood:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
32	CTCF	chr9:96065040-96065190	HUVEC	blood vessel:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
33	CTCF	chr9:96065080-96065230	HPAF	blood vessel:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
34	CTCF	chr9:96065080-96065230	GM12873	blood:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
35	CTCF	chr9:96065100-96065250	GM12872	blood:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
36	CTCF	chr9:96064778-96065466	HCT-116	colon:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
37	RAD21	chr9:96064737-96065363	HCT-116	colon:	n/a	chr9:96064941-96064953 chr9:96065137-96065156
38	SMC3	chr9:96064953-96065336	HepG2	liver:	n/a	chr9:96065141-96065155
39	CTCF	chr9:96064959-96065273	A549	lung:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
40	CTCF	chr9:96064995-96065269	T-47D	breast:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
41	CTCF	chr9:96065060-96065210	HepG2	liver:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
42	ZNF384	chr9:96065086-96065309	GM12878	blood:	n/a	n/a
43	SMC3	chr9:96064955-96065316	K562	blood:	n/a	chr9:96065141-96065155
44	CTCF	chr9:96065040-96065190	GM06990	blood:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
45	USF1	chr9:96065050-96065342	K562	blood:	n/a	chr9:96065174-96065185
46	CTCF	chr9:96064955-96065347	GM12878	blood:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
47	MAZ	chr9:96064920-96065361	IMR90	lung:	n/a	n/a
48	ZNF143	chr9:96064977-96065307	GM12878	blood:	n/a	chr9:96065031-96065050 chr9:96065036-96065054
49	CTCF	chr9:96064993-96065301	MCF-7	breast:	n/a	chr9:96065140-96065156 chr9:96065139-96065157
50	CTCF	chr9:96065100-96065250	HPF	lung:	n/a	chr9:96065140-96065156 chr9:96065139-96065157

No.	Distal block	Cell Line	Cell type
1	chr9:95977876..95978624-chr9:96064689..96065566,3	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	chr9:95926911..95927780-chr9:96064843..96065564,2	MCF-7	breast:
5	chr9:95921857..95922911-chr9:96064779..96065588,5	MCF-7	breast:
6	chr9:95895149..95897720-chr9:96064808..96066436,2	MCF-7	breast:
7	chr9:95921936..95922821-chr9:96064640..96065645,10	MCF-7	breast:
8	chr9:96063114..96067393-chr9:96338286..96340131,3	MCF-7	breast:
9	chr9:95953204..95955785-chr9:96063844..96066566,2	MCF-7	breast:

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

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10122466	0.84[AMR][1000 genomes]
rs10512233	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1539670	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs16909005	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];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16936750	0.89[EUR][1000 genomes]
rs16936752	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1891971	1.00[CEU][hapmap]
rs1891972	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs1891973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs1936403	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1970622	0.84[AMR][1000 genomes]
rs4744197	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4744202	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4744205	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs55643343	0.85[EUR][1000 genomes]
rs55692827	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55706397	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55795421	0.89[EUR][1000 genomes]
rs56300939	0.85[EUR][1000 genomes]
rs59491442	0.83[EUR][1000 genomes]
rs6479467	0.84[AMR][1000 genomes]
rs7029968	1.00[CHB][hapmap]
rs72743431	0.91[AMR][1000 genomes]
rs72743433	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72743435	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72743442	0.89[EUR][1000 genomes]
rs72743443	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72743444	0.88[EUR][1000 genomes]
rs72743445	0.83[EUR][1000 genomes]
rs72743446	0.83[EUR][1000 genomes]
rs72743448	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72743449	0.88[EUR][1000 genomes]
rs72743451	0.83[EUR][1000 genomes]
rs7859604	0.84[AMR][1000 genomes]
rs7859628	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs7871272	1.00[CEU][hapmap];0.84[AMR][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:60 , 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	chr9:96061800-96065200	Strong transcription	Fetal Stomach	stomach
22	chr9:96061800-96066200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:96062000-96066600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:96062400-96065600	Enhancers	HepG2	liver
25	chr9:96062600-96069200	Enhancers	Fetal Muscle Leg	muscle
26	chr9:96063000-96065200	Enhancers	Spleen	Spleen
27	chr9:96063000-96070200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:96063200-96066800	Weak transcription	Psoas Muscle	Psoas
29	chr9:96063200-96072200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:96063400-96067400	Weak transcription	Adipose Nuclei	Adipose
31	chr9:96063400-96069200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:96063600-96065200	Enhancers	Placenta	Placenta
33	chr9:96063600-96070600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr9:96063800-96066000	Weak transcription	Fetal Heart	heart
35	chr9:96063800-96067000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr9:96063800-96067400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:96063800-96088600	Weak transcription	Right Atrium	heart
38	chr9:96064000-96065200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr9:96064000-96066000	Enhancers	Fetal Thymus	thymus
40	chr9:96064000-96066400	Weak transcription	Right Ventricle	heart
41	chr9:96064200-96065200	Enhancers	Primary B cells from cord blood	blood
42	chr9:96064200-96065800	Weak transcription	Fetal Brain Female	brain
43	chr9:96064400-96065200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:96064600-96065200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:96064600-96065200	Enhancers	Primary B cells from peripheral blood	blood
46	chr9:96064600-96065200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr9:96064600-96065600	Weak transcription	Brain Germinal Matrix	brain
48	chr9:96064800-96065200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr9:96064800-96065200	Enhancers	Stomach Mucosa	stomach
50	chr9:96064800-96065400	Genic enhancers	Fetal Intestine Small	intestine

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