Variant report

Variant	rs2989519
Chromosome Location	chr9:117844239-117844240
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	chr9:117843493..117846362-chr9:117847187..117851097,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1061494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250019	0.87[GIH][hapmap]
rs1250023	0.80[JPT][hapmap]
rs1271449	0.96[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1272041	0.88[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1330360	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1360291	0.80[JPT][hapmap]
rs1511	0.87[GIH][hapmap]
rs1617917	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1755637	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755641	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757100	0.80[JPT][hapmap]
rs1757108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757109	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1757110	1.00[ASN][1000 genomes]
rs1757111	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274836	0.87[GIH][hapmap]
rs2480933	0.81[ASW][hapmap]
rs2482077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482078	0.80[JPT][hapmap]
rs2988578	0.80[JPT][hapmap]
rs2992147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789867	0.82[GIH][hapmap]
rs3789868	0.82[GIH][hapmap]
rs769331	0.82[GIH][hapmap]
rs944510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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

No data

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	chr9:117831800-117848000	Strong transcription	Stomach Smooth Muscle	stomach
14	chr9:117834000-117849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:117834000-117849800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:117834800-117848600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:117836000-117848600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:117837000-117844400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:117837000-117849400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:117838800-117846400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:117839000-117846800	Weak transcription	Esophagus	oesophagus
22	chr9:117839000-117848800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:117839000-117849200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:117839600-117849200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:117839800-117847000	Strong transcription	Colon Smooth Muscle	Colon
26	chr9:117840600-117846400	Weak transcription	Aorta	Aorta
27	chr9:117840600-117848000	Weak transcription	Fetal Intestine Large	intestine
28	chr9:117840800-117848600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
30	chr9:117841400-117849200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:117842000-117844400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:117842400-117845800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:117842600-117850400	Weak transcription	Fetal Brain Female	brain
34	chr9:117842800-117849400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:117842800-117855200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:117843200-117844400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:117843200-117845200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:117843200-117846600	Strong transcription	NHEK	skin
39	chr9:117843400-117845600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:117843400-117845600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:117843600-117844600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr9:117843600-117845200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:117843600-117845200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr9:117843600-117845200	Strong transcription	Fetal Stomach	stomach
45	chr9:117843600-117846800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:117843600-117849000	Strong transcription	Fetal Muscle Leg	muscle
47	chr9:117843600-117849400	Strong transcription	NHLF	lung
48	chr9:117844000-117845800	Strong transcription	HMEC	breast
49	chr9:117844200-117845600	Strong transcription	Fetal Lung	lung

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