Variant report

Variant	rs3780416
Chromosome Location	chr9:100674565-100674566
allele	C/T
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:2)
LncRNA
region (count:1)
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	chr9:100674163-100674578	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100674231..100678302-chr9:100744904..100747134,4	MCF-7	breast:
2	chr9:100663583..100665725-chr9:100672529..100674637,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HEMGN-3	chr9:100674292-100674605	l_3819_chr9:100671099-100674605_testes

No data

Variant related genes	Relation type
ENSG00000201830	TF binding region
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10760021	0.84[JPT][hapmap]
rs10984193	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10984297	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10984349	0.95[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];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10984375	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10984405	0.83[ASN][1000 genomes]
rs10984462	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10984478	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10984484	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10984499	0.81[ASN][1000 genomes]
rs10984588	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10984599	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1127703	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12235434	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236440	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237296	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377604	0.84[ASN][1000 genomes]
rs1475695	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1475696	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs17346310	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17431614	0.97[ASN][1000 genomes]
rs17431934	0.84[ASN][1000 genomes]
rs2120263	0.86[YRI][hapmap]
rs2282192	0.86[YRI][hapmap]
rs3780417	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780418	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780419	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3824496	0.97[ASN][1000 genomes]
rs4498663	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4618817	0.95[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4743145	0.97[ASN][1000 genomes]
rs62574034	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62574035	0.86[EUR][1000 genomes]
rs66990486	0.97[ASN][1000 genomes]
rs67500034	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67975003	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68053069	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68112593	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7024281	0.88[AMR][1000 genomes]
rs7025609	0.95[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7030887	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7030907	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7040232	0.89[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72753548	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72753572	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72753587	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs755109	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7855917	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7861658	0.97[ASN][1000 genomes]
rs7864655	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3780416	C9orf156	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:100665400-100679000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:100665600-100678200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:100666600-100675400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:100666600-100676000	Strong transcription	Fetal Intestine Large	intestine
7	chr9:100666800-100675800	Strong transcription	Fetal Stomach	stomach
8	chr9:100667000-100675800	Strong transcription	Fetal Intestine Small	intestine
9	chr9:100667200-100679400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:100667200-100684200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:100669000-100674600	Weak transcription	HUVEC	blood vessel
12	chr9:100669400-100675800	Strong transcription	Brain Germinal Matrix	brain
13	chr9:100669400-100675800	Strong transcription	Fetal Muscle Leg	muscle
14	chr9:100669600-100678600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
15	chr9:100669600-100678800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr9:100669800-100674800	Genic enhancers	Primary T cells from cord blood	blood
17	chr9:100669800-100675400	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr9:100669800-100676400	Strong transcription	K562	blood
19	chr9:100669800-100678400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:100670000-100676200	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:100670000-100678600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr9:100670000-100684200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:100670200-100675400	Strong transcription	Brain Substantia Nigra	brain
24	chr9:100670200-100675800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr9:100670200-100678600	Strong transcription	Liver	Liver
26	chr9:100670200-100678600	Strong transcription	Placenta	Placenta
27	chr9:100670200-100678600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr9:100670400-100675600	Strong transcription	Brain Hippocampus Middle	brain
29	chr9:100670400-100677000	Strong transcription	GM12878-XiMat	blood
30	chr9:100670400-100678400	Strong transcription	Dnd41	blood
31	chr9:100670400-100679400	Strong transcription	Thymus	Thymus
32	chr9:100670600-100676000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:100670800-100684200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr9:100671000-100674600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:100671000-100675000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:100671000-100676200	Strong transcription	Left Ventricle	heart
37	chr9:100671000-100677400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:100671000-100677800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:100671000-100678400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:100671200-100674600	Strong transcription	Brain Cingulate Gyrus	brain
41	chr9:100671200-100675600	Strong transcription	Rectal Smooth Muscle	rectum
42	chr9:100671200-100676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:100671200-100676400	Strong transcription	Brain Angular Gyrus	brain
44	chr9:100671200-100676600	Strong transcription	Adipose Nuclei	Adipose
45	chr9:100671200-100680200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr9:100671400-100675200	Strong transcription	Brain Anterior Caudate	brain
47	chr9:100671400-100676400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr9:100671400-100678800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:100671600-100675000	Strong transcription	Small Intestine	intestine
50	chr9:100671600-100675200	Strong transcription	Ovary	ovary

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