Variant report

Variant	rs1411456
Chromosome Location	chr9:117803882-117803883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10759753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330363	0.86[JPT][hapmap]
rs1330364	0.86[JPT][hapmap]
rs13321	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1411461	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1537017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1547691	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs1547692	0.86[JPT][hapmap]
rs16932078	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1854707	0.86[JPT][hapmap]
rs1888221	0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs2009023	0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2104772	0.82[JPT][hapmap]
rs2210108	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2297180	0.86[JPT][hapmap]
rs3789870	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3789872	0.90[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs3789873	0.94[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs4460459	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6478127	0.86[JPT][hapmap]
rs6478128	0.86[JPT][hapmap]
rs7027148	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7030164	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7032224	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7035322	0.84[TSI][hapmap]
rs7875852	0.86[JPT][hapmap]
rs944223	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs944226	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs953288	0.86[JPT][hapmap]
rs955450	1.00[ASW][hapmap];0.90[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][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	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
4	esv1840787	chr9:117787173-117803882	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv1826575	chr9:117787173-117805719	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv519131	chr9:117796986-117804667	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117781800-117808600	Weak transcription	Fetal Intestine Small	intestine
2	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
3	chr9:117789000-117808600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:117792800-117815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:117797400-117807400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
7	chr9:117798200-117805000	Weak transcription	HSMM	muscle
8	chr9:117798600-117804200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:117798800-117804800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:117799200-117805000	Weak transcription	HSMMtube	muscle
11	chr9:117799200-117819800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:117799400-117817000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:117799800-117804600	Strong transcription	NHEK	skin
14	chr9:117800000-117806600	Strong transcription	NH-A	brain
15	chr9:117800600-117808600	Weak transcription	Fetal Intestine Large	intestine
16	chr9:117800800-117804200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:117800800-117804600	Strong transcription	Osteobl	bone
18	chr9:117800800-117805200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:117800800-117805600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:117800800-117825000	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:117800800-117825200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:117801000-117804400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:117801000-117812400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:117801000-117819200	Weak transcription	HMEC	breast
25	chr9:117801800-117820200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
27	chr9:117802400-117806000	Genic enhancers	Colon Smooth Muscle	Colon
28	chr9:117802600-117812400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:117803200-117805000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:117803200-117808600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:117803400-117804600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:117803400-117804600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:117803400-117804600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:117803400-117805600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:117803400-117805800	Weak transcription	Fetal Stomach	stomach
36	chr9:117803400-117806200	Weak transcription	Fetal Lung	lung
37	chr9:117803400-117808400	Weak transcription	NHLF	lung
38	chr9:117803400-117810400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:117803400-117812000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:117803400-117820000	Weak transcription	Aorta	Aorta
41	chr9:117803400-117820600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:117803600-117804400	Weak transcription	NHDF-Ad	bronchial
43	chr9:117803600-117805200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:117803600-117806400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr9:117803600-117808200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:117803600-117820200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:117803600-117825400	Weak transcription	Fetal Kidney	kidney
48	chr9:117803800-117804400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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