Variant report

Variant	rs12235316
Chromosome Location	chr9:97677556-97677557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:97677454-97677613	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
2	chr9:97572097..97590438-chr9:97672990..97690806,63	MCF-7	breast:
3	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
4	chr9:97640729..97643418-chr9:97677399..97680018,2	MCF-7	breast:
5	chr9:97674629..97677870-chr9:97679171..97683361,5	K562	blood:
6	chr9:97654596..97658293-chr9:97673712..97678137,5	MCF-7	breast:
7	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:
8	chr9:97673705..97676027-chr9:97676375..97678857,2	K562	blood:
9	chr9:97646214..97649715-chr9:97676410..97681725,5	MCF-7	breast:
10	chr9:97665297..97668002-chr9:97676455..97679387,2	MCF-7	breast:
11	chr9:97668825..97671270-chr9:97677329..97679201,2	MCF-7	breast:

No data

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction
ENSG00000252153	Chromatin interaction
ENSG00000230815	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10821415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10993365	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10993370	0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs10993372	0.96[CEU][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10993377	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10993394	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993398	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993418	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1123534	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11787821	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs183066	0.92[CEU][hapmap];0.84[YRI][hapmap]
rs2183958	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2584806	0.92[CEU][hapmap];0.84[YRI][hapmap]
rs35487382	0.81[EUR][1000 genomes]
rs356131	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[YRI][hapmap]
rs391784	0.96[CEU][hapmap];0.84[YRI][hapmap]
rs4385527	0.96[CEU][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs446540	0.92[CEU][hapmap]
rs4744378	0.96[CEU][hapmap];0.92[YRI][hapmap]
rs4744403	0.96[CEU][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744411	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7851726	0.92[CEU][hapmap]
rs7853195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7864171	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7865239	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7866848	0.92[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97661600-97686200	Weak transcription	Primary T cells from cord blood	blood
3	chr9:97662400-97678600	Enhancers	Brain Substantia Nigra	brain
4	chr9:97662600-97680400	Enhancers	Brain Hippocampus Middle	brain
5	chr9:97666000-97678600	Enhancers	Brain Cingulate Gyrus	brain
6	chr9:97669000-97678200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:97669200-97678400	Enhancers	Fetal Heart	heart
8	chr9:97669800-97678200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:97670000-97678600	Weak transcription	Fetal Thymus	thymus
10	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:97670800-97680600	Weak transcription	Ovary	ovary
12	chr9:97671000-97684200	Weak transcription	Small Intestine	intestine
13	chr9:97671600-97681600	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:97671800-97678600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:97672400-97678000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:97672600-97678200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr9:97672600-97680600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr9:97672800-97677600	Weak transcription	Fetal Stomach	stomach
19	chr9:97672800-97678200	Enhancers	HepG2	liver
20	chr9:97673000-97677800	Weak transcription	Gastric	stomach
21	chr9:97673000-97678600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:97673000-97681600	Weak transcription	Spleen	Spleen
23	chr9:97673200-97678000	Enhancers	HSMMtube	muscle
24	chr9:97673600-97677800	Enhancers	HMEC	breast
25	chr9:97674200-97681600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:97674200-97681600	Enhancers	Placenta	Placenta
27	chr9:97674400-97678200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr9:97674400-97678600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr9:97674400-97678600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr9:97674600-97678200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:97674600-97678200	Enhancers	Left Ventricle	heart
32	chr9:97674600-97679600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:97674800-97677800	Enhancers	Brain Angular Gyrus	brain
34	chr9:97674800-97677800	Enhancers	HUVEC	blood vessel
35	chr9:97674800-97678000	Enhancers	NHLF	lung
36	chr9:97674800-97678200	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr9:97674800-97678200	Enhancers	Stomach Mucosa	stomach
38	chr9:97675000-97684400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr9:97675200-97677800	Weak transcription	Esophagus	oesophagus
40	chr9:97675200-97678000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr9:97675200-97678200	Enhancers	HSMM	muscle
42	chr9:97675200-97679400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:97675200-97679400	Weak transcription	Fetal Lung	lung
44	chr9:97675200-97681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:97675400-97681000	Enhancers	Hela-S3	cervix
46	chr9:97675400-97684000	Weak transcription	Psoas Muscle	Psoas
47	chr9:97675600-97677800	Enhancers	Fetal Intestine Small	intestine
48	chr9:97675800-97678000	Enhancers	Fetal Intestine Large	intestine
49	chr9:97675800-97678200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr9:97676200-97677600	Weak transcription	Brain Germinal Matrix	brain

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