Variant report

Variant	rs1330349
Chromosome Location	chr9:117840742-117840743
allele	C/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	POLR2A	chr9:117840735-117842415	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:117834838..117836776-chr9:117839002..117841369,2	K562	blood:
2	chr9:117839179..117841856-chr9:117845552..117848001,2	MCF-7	breast:
3	chr9:117840344..117843174-chr9:117844856..117847234,2	K562	blood:
4	chr9:117840344..117843174-chr9:117844856..117847663,3	K562	blood:

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

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1250023	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1250026	0.92[CEU][hapmap]
rs1273108	0.92[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs1330350	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330351	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1330360	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1360291	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1757100	0.88[CEU][hapmap]
rs1929395	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2482078	0.88[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs2482080	0.92[CEU][hapmap]
rs2988578	0.92[CEU][hapmap]
rs2989518	0.92[CEU][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1330349	DFNB31	cis	cerebellum	SCAN
rs1330349	C9orf91	cis	cerebellum	SCAN
rs1330349	ATP6V1G1	cis	cerebellum	SCAN
rs1330349	C9orf80	cis	cerebellum	SCAN
rs1330349	SNX30	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
3	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117817800-117850600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:117819800-117848000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:117822400-117854400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:117825400-117848000	Weak transcription	Lung	lung
8	chr9:117826800-117849400	Strong transcription	Osteobl	bone
9	chr9:117827000-117848600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:117827000-117849200	Strong transcription	NHDF-Ad	bronchial
11	chr9:117827200-117855200	Strong transcription	NH-A	brain
12	chr9:117827400-117849200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:117830400-117840800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:117831800-117848000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr9:117832400-117842400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:117834000-117849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:117834000-117849800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:117834200-117842000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:117834800-117848600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr9:117835000-117842400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:117835800-117841800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:117836000-117848600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:117837000-117844400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:117837000-117849400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:117838800-117844000	Weak transcription	HMEC	breast
26	chr9:117838800-117846400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:117839000-117840800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:117839000-117841000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:117839000-117841400	Weak transcription	Fetal Lung	lung
30	chr9:117839000-117843200	Weak transcription	NHEK	skin
31	chr9:117839000-117846800	Weak transcription	Esophagus	oesophagus
32	chr9:117839000-117848800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:117839000-117849200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:117839400-117842200	Weak transcription	Liver	Liver
35	chr9:117839600-117849200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:117839800-117841400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:117839800-117847000	Strong transcription	Colon Smooth Muscle	Colon
38	chr9:117840000-117842200	Strong transcription	NHLF	lung
39	chr9:117840200-117841200	Strong transcription	Fetal Kidney	kidney
40	chr9:117840200-117842000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:117840400-117841200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:117840400-117843600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr9:117840400-117843600	Weak transcription	Fetal Muscle Leg	muscle
44	chr9:117840600-117842800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:117840600-117843400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:117840600-117843600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:117840600-117843600	Weak transcription	Fetal Stomach	stomach
48	chr9:117840600-117846400	Weak transcription	Aorta	Aorta
49	chr9:117840600-117848000	Weak transcription	Fetal Intestine Large	intestine

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