Variant report

Variant	rs10817709
Chromosome Location	chr9:117850562-117850563
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117843493..117846362-chr9:117847187..117851097,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10120799	1.00[CEU][hapmap]
rs10122188	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs10125919	1.00[CEU][hapmap]
rs10817710	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817711	0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817719	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs10817720	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs10817726	0.82[YRI][hapmap]
rs10982516	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10982518	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]
rs10982519	1.00[CEU][hapmap];0.83[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];0.97[ASN][1000 genomes]
rs10982530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10982531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10982532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10982538	0.94[ASN][1000 genomes]
rs10982539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10982585	0.81[CEU][hapmap]
rs10982589	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs10982590	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs10982592	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs10982597	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs12001569	0.82[YRI][hapmap]
rs12235159	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12238613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12238717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12340324	0.90[CEU][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12346640	0.88[CEU][hapmap]
rs1335334	0.82[YRI][hapmap]
rs16932349	0.82[YRI][hapmap]
rs3827815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59939445	0.94[ASN][1000 genomes]
rs6478141	0.81[CEU][hapmap]
rs6478143	0.81[CEU][hapmap]
rs7027235	0.81[CEU][hapmap]
rs7030384	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs7048739	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs7847093	0.81[CEU][hapmap]
rs7851019	0.81[CEU][hapmap]
rs7851086	0.80[CEU][hapmap]
rs7862558	0.81[CEU][hapmap]
rs7866441	0.81[CEU][hapmap]
rs9886855	0.90[CEU][hapmap];0.82[YRI][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

No data

Chromatin state (count:49 , 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	chr9:117817800-117850600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:117822400-117854400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:117827200-117855200	Strong transcription	NH-A	brain
5	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
6	chr9:117842800-117855200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:117846600-117851000	Weak transcription	Right Atrium	heart
8	chr9:117847200-117856000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:117848600-117850600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:117848600-117851000	Strong transcription	Colon Smooth Muscle	Colon
11	chr9:117848800-117852800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:117849000-117856400	Weak transcription	Brain Substantia Nigra	brain
13	chr9:117849200-117850800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:117849200-117850800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:117849200-117851200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:117849200-117851600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:117849200-117851600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:117849200-117851600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:117849200-117851800	Genic enhancers	NHDF-Ad	bronchial
20	chr9:117849400-117850800	Genic enhancers	NHLF	lung
21	chr9:117849400-117851600	Genic enhancers	Osteobl	bone
22	chr9:117849400-117852000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr9:117849400-117852800	Weak transcription	Fetal Intestine Large	intestine
24	chr9:117849400-117853200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:117849400-117855400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:117849400-117855600	Weak transcription	Fetal Lung	lung
27	chr9:117849400-117856200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr9:117849400-117856800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
30	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:117849600-117851200	Enhancers	NHEK	skin
32	chr9:117849600-117851400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:117849600-117851400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:117849600-117851400	Weak transcription	Fetal Intestine Small	intestine
35	chr9:117849600-117852000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:117849600-117852400	Weak transcription	Fetal Stomach	stomach
37	chr9:117849600-117852600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:117849600-117856400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:117849600-117857000	Weak transcription	Spleen	Spleen
40	chr9:117849600-117864600	Weak transcription	HMEC	breast
41	chr9:117849800-117850800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr9:117849800-117851600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:117849800-117852600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:117849800-117854600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:117849800-117860400	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:117849800-117860600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:117850000-117852000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:117850400-117851800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:117850400-117853400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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