Variant report

Variant	rs2169643
Chromosome Location	chr3:110889974-110889975
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11929280	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs12485668	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1477841	0.85[CEU][hapmap]
rs1477842	0.85[CEU][hapmap]
rs1477843	0.85[CEU][hapmap]
rs1477846	0.85[CEU][hapmap];0.88[MKK][hapmap]
rs1477847	0.85[CEU][hapmap]
rs1477848	0.85[CEU][hapmap];0.85[MKK][hapmap]
rs1477850	1.00[CEU][hapmap]
rs2126713	0.85[CEU][hapmap]
rs2399373	0.85[CEU][hapmap]
rs2399375	0.85[CEU][hapmap]
rs2399376	0.94[AFR][1000 genomes]
rs35441599	0.92[AFR][1000 genomes]
rs4682229	0.85[CEU][hapmap]
rs4682230	0.85[CEU][hapmap]
rs4682231	0.85[CEU][hapmap]
rs4682234	0.85[CEU][hapmap]
rs4682238	0.85[CEU][hapmap]
rs4682240	0.87[AMR][1000 genomes]
rs6437948	0.85[CEU][hapmap]
rs6437953	0.85[CEU][hapmap]
rs6794645	0.85[CEU][hapmap]
rs7430600	0.85[CEU][hapmap]
rs7432996	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433877	1.00[CEU][hapmap]
rs7610754	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7610760	0.85[CEU][hapmap]
rs7612667	0.85[CEU][hapmap]
rs7620372	0.89[ASW][hapmap];0.82[CEU][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes]
rs7623880	0.85[CEU][hapmap]
rs7648752	1.00[CEU][hapmap]
rs7653595	0.85[CEU][hapmap]
rs873132	1.00[CEU][hapmap]
rs9288918	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs9821335	0.85[CEU][hapmap]
rs9828899	0.85[CEU][hapmap]
rs9866028	0.85[CEU][hapmap]
rs9876350	0.85[CEU][hapmap]
rs9882945	1.00[CEU][hapmap]

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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv829675	chr3:110885605-111101858	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv877339	chr3:110889974-111070554	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110816000-110893400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:110829400-110893400	Weak transcription	HUVEC	blood vessel
3	chr3:110832200-110892400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:110832400-110911200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:110834000-110891800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:110835600-110929600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:110842600-110911200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:110847000-110911400	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:110848200-110891800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:110853000-110919600	Weak transcription	Fetal Brain Male	brain
11	chr3:110853200-110897000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:110853200-110911000	Weak transcription	NH-A	brain
13	chr3:110857800-110892000	Weak transcription	Adipose Nuclei	Adipose
14	chr3:110864200-110891800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:110869400-110929000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:110870200-110891800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:110871000-110914200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:110871200-110896400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:110871600-110892200	Weak transcription	NHLF	lung
20	chr3:110872200-110913800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:110872600-110918800	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:110872800-110893400	Weak transcription	Gastric	stomach
23	chr3:110872800-110896000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:110874200-110893400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:110874200-110893400	Weak transcription	Fetal Intestine Small	intestine
26	chr3:110874200-110894200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:110874200-110912000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:110874400-110911800	Weak transcription	Left Ventricle	heart
29	chr3:110874800-110891600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:110874800-110913000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:110875000-110891600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:110875200-110897600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:110877800-110891600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:110880600-110892000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:110880600-110903600	Weak transcription	Fetal Kidney	kidney
36	chr3:110880800-110890800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:110880800-110892800	Weak transcription	Fetal Stomach	stomach
38	chr3:110881000-110891800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:110881000-110891800	Weak transcription	HSMMtube	muscle
40	chr3:110881000-110892400	Weak transcription	A549	lung
41	chr3:110881000-110928000	Weak transcription	Osteobl	bone
42	chr3:110882000-110892800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:110882200-110892000	Weak transcription	Fetal Intestine Large	intestine
44	chr3:110882400-110892000	Weak transcription	HepG2	liver
45	chr3:110883800-110908400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:110885200-110891600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:110885400-110891600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:110886400-110892000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:110886800-110890600	Weak transcription	Fetal Lung	lung
50	chr3:110886800-110891800	Weak transcription	Placenta	Placenta

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