Variant report

Variant	rs2992147
Chromosome Location	chr9:117849314-117849315
allele	C/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: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1061494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[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];0.81[LWK][hapmap]
rs1617917	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1755637	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755641	1.00[AFR][1000 genomes];0.99[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];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[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];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757109	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1757110	1.00[ASN][1000 genomes]
rs1757111	0.94[AFR][1000 genomes];0.99[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274836	0.87[GIH][hapmap]
rs2482077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482078	0.80[JPT][hapmap]
rs2988578	0.80[JPT][hapmap]
rs2989519	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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv3481731	chr9:117847681-117850479	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
5	esv3481732	chr9:117847681-117850479	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

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	chr9:117826800-117849400	Strong transcription	Osteobl	bone
5	chr9:117827200-117855200	Strong transcription	NH-A	brain
6	chr9:117834000-117849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:117834000-117849800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:117837000-117849400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
10	chr9:117842600-117850400	Weak transcription	Fetal Brain Female	brain
11	chr9:117842800-117849400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:117842800-117855200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:117843600-117849400	Strong transcription	NHLF	lung
14	chr9:117845600-117850000	Weak transcription	Gastric	stomach
15	chr9:117845800-117849600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:117845800-117850400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:117846200-117849600	Strong transcription	Fetal Stomach	stomach
18	chr9:117846200-117849800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:117846200-117849800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:117846600-117849600	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:117846600-117849600	Genic enhancers	NHEK	skin
22	chr9:117846600-117851000	Weak transcription	Right Atrium	heart
23	chr9:117846800-117849600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:117847200-117856000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:117847800-117849600	Genic enhancers	Rectal Smooth Muscle	rectum
26	chr9:117848000-117849400	Strong transcription	Fetal Intestine Large	intestine
27	chr9:117848000-117849600	Strong transcription	Fetal Intestine Small	intestine
28	chr9:117848200-117849600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:117848200-117849600	Strong transcription	Spleen	Spleen
30	chr9:117848400-117849600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:117848600-117849400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:117848600-117849400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr9:117848600-117849400	Strong transcription	Fetal Lung	lung
34	chr9:117848600-117850000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr9:117848600-117850600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:117848600-117851000	Strong transcription	Colon Smooth Muscle	Colon
37	chr9:117848800-117849400	ZNF genes & repeats	Aorta	Aorta
38	chr9:117848800-117849800	Weak transcription	Lung	lung
39	chr9:117848800-117850400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:117848800-117852800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:117849000-117849400	Enhancers	Fetal Muscle Trunk	muscle
42	chr9:117849000-117849400	Genic enhancers	Fetal Muscle Leg	muscle
43	chr9:117849000-117849400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
44	chr9:117849000-117849400	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr9:117849000-117849600	Enhancers	Esophagus	oesophagus
46	chr9:117849000-117856400	Weak transcription	Brain Substantia Nigra	brain
47	chr9:117849200-117849400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
48	chr9:117849200-117849600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr9:117849200-117849600	Enhancers	HMEC	breast
50	chr9:117849200-117850400	Enhancers	Muscle Satellite Cultured Cells	--

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