Variant report

Variant	rs1330363
Chromosome Location	chr9:117813990-117813991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117808226..117809818-chr9:117811512..117814202,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10123436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759752	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs10817705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411456	0.86[JPT][hapmap]
rs1411461	0.86[JPT][hapmap]
rs1537017	0.86[JPT][hapmap]
rs1547691	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1547692	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1854707	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1888222	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2009023	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2104772	0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2297180	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789872	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3789873	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4460459	0.86[JPT][hapmap]
rs6478127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478128	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7030164	0.86[JPT][hapmap]
rs7865462	0.81[MKK][hapmap]
rs7875852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944223	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs944226	0.86[JPT][hapmap]
rs953288	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1330363	COL27A1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:117792800-117815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117799200-117819800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:117799400-117817000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:117800800-117825000	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:117800800-117825200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:117801000-117819200	Weak transcription	HMEC	breast
9	chr9:117801800-117820200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
11	chr9:117803400-117820000	Weak transcription	Aorta	Aorta
12	chr9:117803400-117820600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:117803600-117820200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:117803600-117825400	Weak transcription	Fetal Kidney	kidney
15	chr9:117805800-117818800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:117806800-117816800	Strong transcription	Osteobl	bone
17	chr9:117807200-117816800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:117807400-117819600	Strong transcription	NHDF-Ad	bronchial
19	chr9:117807400-117819800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:117807600-117817400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:117808600-117815000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:117809000-117825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:117809200-117821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:117809400-117815000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:117809800-117815200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:117810000-117817600	Weak transcription	Fetal Stomach	stomach
27	chr9:117810200-117817600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:117810600-117825000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:117810800-117814400	Weak transcription	NHLF	lung
30	chr9:117811000-117816600	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:117811800-117816800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:117812000-117814200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:117812800-117819200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:117812800-117825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:117812800-117830600	Weak transcription	Fetal Lung	lung
36	chr9:117813000-117817000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:117813000-117817600	Weak transcription	NHEK	skin
38	chr9:117813200-117825000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:117813600-117819200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:117813800-117815000	Weak transcription	NH-A	brain
41	chr9:117813800-117815200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
42	chr9:117813800-117816800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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