Variant report

Variant	rs2972995
Chromosome Location	chr5:42757540-42757541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10038285	0.89[JPT][hapmap]
rs10038477	0.89[JPT][hapmap]
rs10041130	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10044169	0.89[JPT][hapmap]
rs10061833	1.00[JPT][hapmap]
rs10077296	0.89[JPT][hapmap]
rs10941583	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12652476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12654861	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12656017	0.90[ASN][1000 genomes]
rs12658099	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658163	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12659225	0.81[ASN][1000 genomes]
rs1423655	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16872680	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16872694	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16872756	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16872762	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16872777	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16872779	0.81[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs16872791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16872824	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16872825	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16872830	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16872832	0.80[ASN][1000 genomes]
rs17839373	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17839374	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230808	0.97[ASN][1000 genomes]
rs230809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230811	0.94[ASN][1000 genomes]
rs2548719	0.92[ASN][1000 genomes]
rs28918068	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28919894	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28919901	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28919903	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28943887	1.00[EUR][1000 genomes]
rs28943888	1.00[EUR][1000 genomes]
rs2910854	0.97[ASN][1000 genomes]
rs2910860	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2910863	0.97[ASN][1000 genomes]
rs2910866	0.97[ASN][1000 genomes]
rs2910878	0.89[JPT][hapmap]
rs2910879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972752	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972764	0.84[ASN][1000 genomes]
rs2972768	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972769	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972780	0.89[JPT][hapmap]
rs2972782	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972991	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2973004	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973008	0.92[ASN][1000 genomes]
rs2973009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973016	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973019	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34319505	1.00[EUR][1000 genomes]
rs34382565	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35291899	0.82[ASN][1000 genomes]
rs35389780	1.00[EUR][1000 genomes]
rs35436563	1.00[EUR][1000 genomes]
rs35604733	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4146624	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs4242119	0.89[JPT][hapmap]
rs4273617	0.89[JPT][hapmap]
rs4376276	0.89[ASN][1000 genomes]
rs4547964	0.82[JPT][hapmap]
rs4637559	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4866948	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs6179	0.89[JPT][hapmap]
rs6182	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6184	0.91[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7703289	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
9	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
10	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42756600-42757800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr5:42756600-42757800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr5:42756600-42757800	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr5:42756600-42757800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:42756600-42758000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:42756600-42758000	Active TSS	Fetal Brain Female	brain
7	chr5:42756800-42757600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:42756800-42757600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr5:42756800-42757600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr5:42756800-42757600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:42756800-42757600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr5:42756800-42757600	Active TSS	Primary B cells from cord blood	blood
13	chr5:42756800-42757600	Active TSS	Primary T cells from cord blood	blood
14	chr5:42756800-42757600	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr5:42756800-42757600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:42756800-42757600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:42756800-42757600	Active TSS	Brain Substantia Nigra	brain
18	chr5:42756800-42757600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
19	chr5:42756800-42757600	Active TSS	Fetal Kidney	kidney
20	chr5:42756800-42757600	Active TSS	Fetal Stomach	stomach
21	chr5:42756800-42757600	Active TSS	NHEK	skin
22	chr5:42756800-42757800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:42756800-42757800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:42756800-42757800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr5:42756800-42757800	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr5:42756800-42757800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:42756800-42757800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:42756800-42757800	Active TSS	Aorta	Aorta
29	chr5:42756800-42757800	Active TSS	Brain Angular Gyrus	brain
30	chr5:42756800-42757800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:42756800-42757800	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr5:42756800-42757800	Active TSS	Right Atrium	heart
33	chr5:42756800-42757800	Active TSS	Thymus	Thymus
34	chr5:42756800-42757800	Active TSS	HSMMtube	muscle
35	chr5:42756800-42757800	Active TSS	NH-A	brain
36	chr5:42756800-42757800	Active TSS	NHLF	lung
37	chr5:42756800-42758000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:42756800-42758000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
39	chr5:42756800-42758000	Active TSS	Brain Hippocampus Middle	brain
40	chr5:42756800-42758000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr5:42757000-42757600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:42757000-42757600	Bivalent Enhancer	Liver	Liver
43	chr5:42757000-42757600	Active TSS	Duodenum Mucosa	Duodenum
44	chr5:42757000-42757600	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr5:42757000-42757600	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr5:42757000-42757600	Active TSS	Rectal Smooth Muscle	rectum
47	chr5:42757000-42757800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr5:42757000-42757800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:42757000-42757800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:42757000-42757800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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