Variant report

Variant	rs1271449
Chromosome Location	chr9:117852522-117852523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1061494	0.96[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1250023	0.85[CHB][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.85[MKK][hapmap]
rs1272041	0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs1330360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1335351	0.81[MEX][hapmap]
rs1335355	0.82[MEX][hapmap]
rs1360291	0.85[CHB][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap]
rs1414148	0.82[MEX][hapmap]
rs1617917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755637	0.86[ASN][1000 genomes]
rs1755638	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1755640	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1755641	0.86[ASN][1000 genomes]
rs1757096	0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1757100	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs1757108	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1757109	0.85[ASN][1000 genomes]
rs1757110	0.86[ASN][1000 genomes]
rs1757111	0.86[ASN][1000 genomes]
rs1888220	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2480931	0.81[ASN][1000 genomes]
rs2482077	0.96[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2482078	0.85[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap]
rs2988578	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs2989519	0.96[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2992147	0.96[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6478150	0.82[MEX][hapmap]
rs6478153	0.86[MEX][hapmap]
rs7043594	0.82[MEX][hapmap]
rs7043679	0.82[MEX][hapmap]
rs7044001	0.82[MEX][hapmap]
rs944510	0.96[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][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	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
rs1271449	SNX30	cis	cerebellum	SCAN
rs1271449	C9orf80	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:117822400-117854400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:117827200-117855200	Strong transcription	NH-A	brain
4	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
5	chr9:117842800-117855200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:117847200-117856000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:117848800-117852800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:117849000-117856400	Weak transcription	Brain Substantia Nigra	brain
9	chr9:117849400-117852800	Weak transcription	Fetal Intestine Large	intestine
10	chr9:117849400-117853200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:117849400-117855400	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:117849400-117855600	Weak transcription	Fetal Lung	lung
13	chr9:117849400-117856200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:117849400-117856800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
16	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:117849600-117852600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr9:117849600-117856400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:117849600-117857000	Weak transcription	Spleen	Spleen
20	chr9:117849600-117864600	Weak transcription	HMEC	breast
21	chr9:117849800-117852600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:117849800-117854600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:117849800-117860400	Weak transcription	Fetal Muscle Leg	muscle
24	chr9:117849800-117860600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:117850400-117853400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:117850800-117857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:117851200-117867200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:117851400-117853400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:117851600-117853400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:117851600-117853400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:117851600-117854400	Strong transcription	Osteobl	bone
32	chr9:117851600-117854600	Strong transcription	NHEK	skin
33	chr9:117851600-117855600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:117851800-117854000	Strong transcription	NHDF-Ad	bronchial
35	chr9:117851800-117855200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:117852000-117853200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr9:117852000-117853400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:117852000-117853400	Strong transcription	NHLF	lung
39	chr9:117852200-117853200	Strong transcription	Colon Smooth Muscle	Colon
40	chr9:117852200-117853200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:117852400-117853200	Genic enhancers	Rectal Smooth Muscle	rectum
42	chr9:117852400-117853400	Strong transcription	Fetal Stomach	stomach
43	chr9:117852400-117855400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr9:117852400-117857000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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