Variant report

Variant	rs3112990
Chromosome Location	chr2:95750419-95750420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2001254	0.82[ASN][1000 genomes]
rs2291991	0.81[ASN][1000 genomes]
rs2320619	0.81[ASN][1000 genomes]
rs2320620	0.82[ASN][1000 genomes]
rs2320624	0.83[ASN][1000 genomes]
rs3105100	0.94[ASN][1000 genomes]
rs3105101	0.95[ASN][1000 genomes]
rs3105102	0.82[ASN][1000 genomes]
rs3105104	0.82[ASN][1000 genomes]
rs3105105	0.83[ASN][1000 genomes]
rs3112221	0.82[ASN][1000 genomes]
rs3112223	0.82[ASN][1000 genomes]
rs3112225	0.85[ASN][1000 genomes]
rs3112228	0.85[ASN][1000 genomes]
rs3112229	0.82[ASN][1000 genomes]
rs3112230	0.83[ASN][1000 genomes]
rs3112231	0.84[ASN][1000 genomes]
rs3112982	0.81[ASN][1000 genomes]
rs3112983	0.80[ASN][1000 genomes]
rs3112984	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3112985	0.88[ASN][1000 genomes]
rs3112986	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3112987	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3112988	0.92[ASN][1000 genomes]
rs3112995	0.82[ASN][1000 genomes]
rs3112996	0.82[ASN][1000 genomes]
rs3112997	0.82[ASN][1000 genomes]
rs3113000	0.83[ASN][1000 genomes]
rs3113001	0.83[ASN][1000 genomes]
rs4854243	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4854244	0.86[ASN][1000 genomes]
rs6719098	0.81[ASN][1000 genomes]
rs7585473	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs872580	0.81[ASN][1000 genomes]

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	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv963662	chr2:95739492-95770323	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95743000-95750800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:95743000-95751000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:95743000-95751000	Weak transcription	Primary B cells from cord blood	blood
4	chr2:95743000-95751200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:95743000-95753000	Weak transcription	Spleen	Spleen
6	chr2:95743000-95759400	Weak transcription	Right Atrium	heart
7	chr2:95743000-95770200	Weak transcription	Psoas Muscle	Psoas
8	chr2:95743200-95750600	Weak transcription	HMEC	breast
9	chr2:95743200-95750800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:95743200-95750800	Weak transcription	Right Ventricle	heart
11	chr2:95743200-95751000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:95743200-95751000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:95743200-95753000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:95743200-95753000	Weak transcription	Colonic Mucosa	Colon
15	chr2:95743400-95750800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:95743400-95751000	Weak transcription	Liver	Liver
17	chr2:95743400-95751000	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:95743400-95751000	Weak transcription	Lung	lung
19	chr2:95743400-95751200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:95743400-95751200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:95743400-95751200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:95743400-95751400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:95743400-95752000	Weak transcription	GM12878-XiMat	blood
24	chr2:95743400-95752600	Weak transcription	K562	blood
25	chr2:95743400-95753000	Weak transcription	Pancreas	Pancrea
26	chr2:95743600-95750800	Weak transcription	Brain Angular Gyrus	brain
27	chr2:95743600-95751200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:95743600-95751200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:95744000-95751000	Weak transcription	Dnd41	blood
30	chr2:95744000-95751200	Weak transcription	Esophagus	oesophagus
31	chr2:95744200-95751200	Weak transcription	Brain Anterior Caudate	brain
32	chr2:95744400-95750800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:95744600-95750600	Weak transcription	A549	lung
34	chr2:95744600-95751000	Weak transcription	Brain Substantia Nigra	brain
35	chr2:95744800-95751200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:95745000-95751200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:95745200-95750800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:95745200-95751000	Weak transcription	Placenta	Placenta
39	chr2:95745400-95750600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:95745400-95750600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:95745400-95750800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:95745400-95750800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:95745400-95751000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:95745400-95751000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:95745400-95751000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:95745400-95751200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:95745400-95751200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:95745400-95751200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:95745400-95751400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:95745400-95751400	Weak transcription	HepG2	liver

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