Variant report

Variant	rs1330368
Chromosome Location	chr9:117821026-117821027
allele	A/G
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	EP300	chr9:117819592-117821048	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr9:117820902-117821629	U87	brain:	n/a	n/a
3	TCF12	chr9:117819474-117821073	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr9:117819454-117821891	SK-N-SH	brain:	n/a	chr9:117819980-117819996 chr9:117819810-117819817
5	E2F4	chr9:117821020-117821589	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr9:117819241-117822911	U87	brain:	n/a	n/a
7	NFIC	chr9:117819479-117821055	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr9:117819547-117821092	SK-N-SH	brain:	n/a	chr9:117819980-117819996 chr9:117819810-117819817
9	POLR2A	chr9:117821016-117822911	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117816355..117818608-chr9:117819773..117822159,2	K562	blood:

Variant related genes	Relation type
TNC	TF binding region
ENSG00000041982	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1060545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16932160	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2297180	0.82[MKK][hapmap]
rs5010187	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478128	0.82[MKK][hapmap]
rs7865462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs953288	0.82[MKK][hapmap]

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	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1330368	SLC31A1	cis	cerebellum	SCAN
rs1330368	PRPF4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:117800800-117825000	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:117800800-117825200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
6	chr9:117803600-117825400	Weak transcription	Fetal Kidney	kidney
7	chr9:117809000-117825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:117810600-117825000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:117812800-117825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:117812800-117830600	Weak transcription	Fetal Lung	lung
11	chr9:117813200-117825000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:117815200-117825200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:117816000-117825200	Weak transcription	Esophagus	oesophagus
15	chr9:117816800-117825000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr9:117817800-117850600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:117818800-117823200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:117819200-117822400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:117819200-117822600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:117819200-117827400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr9:117819400-117825800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:117819600-117821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:117819600-117822800	Genic enhancers	Osteobl	bone
24	chr9:117819800-117822000	Genic enhancers	NH-A	brain
25	chr9:117819800-117822200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:117819800-117822200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:117819800-117822600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:117819800-117822800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:117819800-117848000	Weak transcription	Fetal Intestine Small	intestine
30	chr9:117820200-117821800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:117820200-117822400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:117820200-117822600	Enhancers	NHDF-Ad	bronchial
33	chr9:117820200-117822800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:117820200-117822800	Genic enhancers	NHLF	lung
35	chr9:117820200-117824600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:117820400-117822200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:117820400-117823400	Enhancers	NHEK	skin
38	chr9:117820600-117821200	Genic enhancers	Colon Smooth Muscle	Colon
39	chr9:117820600-117822400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:117820800-117821200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:117820800-117821200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:117820800-117821600	Weak transcription	HSMM	muscle
43	chr9:117820800-117821800	Weak transcription	Fetal Stomach	stomach
44	chr9:117820800-117823200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:117821000-117821200	Enhancers	HSMMtube	muscle
46	chr9:117821000-117821400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:117821000-117821400	Flanking Active TSS	HMEC	breast
48	chr9:117821000-117821800	Weak transcription	Aorta	Aorta
49	chr9:117821000-117822000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr9:117821000-117822400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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