Variant report

Variant	rs17281647
Chromosome Location	chr3:119148476-119148477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGAP31-2	chr3:119147387-119149420	NONHSAT091384

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1132202	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]
rs11556604	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12631504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16829809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17281612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17281703	0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2282173	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2282175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57509340	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58968288	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59333081	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59551807	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60375691	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60588168	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60671082	0.80[AMR][1000 genomes]
rs61740281	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6772534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6782411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6800924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72968474	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119121200-119150000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:119134200-119148800	Weak transcription	Pancreas	Pancrea
3	chr3:119135200-119149800	Weak transcription	Gastric	stomach
4	chr3:119135400-119150000	Weak transcription	Spleen	Spleen
5	chr3:119138000-119152400	Weak transcription	Lung	lung
6	chr3:119142400-119150800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:119144400-119150400	ZNF genes & repeats	Liver	Liver
8	chr3:119144600-119152000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:119145400-119149600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:119145600-119149000	ZNF genes & repeats	HSMM	muscle
11	chr3:119145600-119149600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:119145600-119150200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:119145600-119150200	ZNF genes & repeats	Fetal Kidney	kidney
14	chr3:119145600-119152000	ZNF genes & repeats	Fetal Lung	lung
15	chr3:119145800-119150200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr3:119145800-119151000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr3:119145800-119151800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:119146000-119149400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
19	chr3:119146200-119149000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr3:119146400-119150400	ZNF genes & repeats	Fetal Muscle Leg	muscle
21	chr3:119146400-119150600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:119146400-119150600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr3:119146600-119148600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
24	chr3:119146600-119149400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
25	chr3:119146600-119149400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
26	chr3:119146600-119150200	ZNF genes & repeats	A549	lung
27	chr3:119146600-119150600	ZNF genes & repeats	Dnd41	blood
28	chr3:119146600-119151000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:119146800-119148800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:119146800-119149400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:119146800-119149400	ZNF genes & repeats	Brain Germinal Matrix	brain
32	chr3:119146800-119150000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
33	chr3:119147000-119150600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
34	chr3:119147000-119151800	Strong transcription	NH-A	brain
35	chr3:119147000-119152800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:119147000-119179000	Strong transcription	Osteobl	bone
37	chr3:119147200-119148600	ZNF genes & repeats	Fetal Brain Male	brain
38	chr3:119147200-119148600	Weak transcription	HUVEC	blood vessel
39	chr3:119147200-119150400	ZNF genes & repeats	Fetal Intestine Large	intestine
40	chr3:119147200-119150400	ZNF genes & repeats	GM12878-XiMat	blood
41	chr3:119147200-119150600	ZNF genes & repeats	Fetal Brain Female	brain
42	chr3:119147200-119152200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr3:119147200-119180400	Weak transcription	Stomach Mucosa	stomach
44	chr3:119147400-119148800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
45	chr3:119147400-119149200	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr3:119147400-119150200	ZNF genes & repeats	NHEK	skin
47	chr3:119147400-119150400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
48	chr3:119147400-119150400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
49	chr3:119147400-119150600	ZNF genes & repeats	Primary T cells from cord blood	blood
50	chr3:119147400-119151000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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