Variant report

Variant	rs4979240
Chromosome Location	chr9:116127472-116127473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116125894..116128604-chr9:116186096..116187911,2	K562	blood:
2	chr9:116125138..116127996-chr9:116129478..116132469,3	K562	blood:
3	chr9:116124299..116128919-chr9:116129296..116133206,5	K562	blood:
4	chr9:116108846..116117047-chr9:116126327..116140994,30	MCF-7	breast:
5	chr9:116127286..116129224-chr9:116135348..116138252,2	K562	blood:
6	chr9:116116183..116118289-chr9:116124994..116127482,2	K562	blood:

Variant related genes	Relation type
ENSG00000119411	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1077636	0.89[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs10981766	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981767	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981768	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981769	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981770	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981773	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347607	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352548	0.94[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3763667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4979239	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4979241	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4979242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55687303	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55753822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478009	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031690	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033437	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037201	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7037702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038037	0.85[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap]
rs7041125	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045901	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045908	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs752758	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7864273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv519849	chr9:116111407-116144973	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1036586	chr9:116118902-116136993	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv615214	chr9:116125789-116149967	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4979240	SLC31A1	cis	parietal	SCAN
rs4979240	DEC1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116113000-116135600	Weak transcription	Colonic Mucosa	Colon
2	chr9:116113000-116138000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:116113400-116135200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:116113800-116137800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:116114200-116136400	Weak transcription	Primary B cells from cord blood	blood
6	chr9:116115400-116135000	Weak transcription	Esophagus	oesophagus
7	chr9:116115600-116132800	Weak transcription	Fetal Intestine Large	intestine
8	chr9:116116400-116137000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:116120200-116131800	Weak transcription	Lung	lung
10	chr9:116123000-116132800	Weak transcription	Fetal Stomach	stomach
11	chr9:116123200-116129200	Enhancers	Hela-S3	cervix
12	chr9:116123200-116131800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:116123200-116136400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr9:116123600-116138200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr9:116123800-116130400	Weak transcription	Stomach Mucosa	stomach
16	chr9:116124000-116135000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:116124000-116135000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:116124000-116135600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:116124000-116135600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:116124200-116127800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:116124400-116128400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:116124400-116131600	Weak transcription	Pancreas	Pancrea
23	chr9:116124400-116135600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:116124800-116128800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:116124800-116134200	Weak transcription	Brain Anterior Caudate	brain
26	chr9:116124800-116134400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:116124800-116135000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:116124800-116135200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:116124800-116135400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:116124800-116135800	Weak transcription	Brain Substantia Nigra	brain
31	chr9:116125000-116130600	Weak transcription	Gastric	stomach
32	chr9:116125000-116138000	Weak transcription	Fetal Kidney	kidney
33	chr9:116125200-116133600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:116125200-116135000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:116125800-116128200	Enhancers	K562	blood
36	chr9:116126200-116134400	Weak transcription	Placenta	Placenta
37	chr9:116126400-116128200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:116126400-116128600	Weak transcription	Fetal Intestine Small	intestine
39	chr9:116126800-116133200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:116127200-116127800	Enhancers	Fetal Heart	heart
41	chr9:116127200-116128400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr9:116127400-116127800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr9:116127400-116128400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr9:116127400-116128800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr9:116127400-116128800	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links