Variant report

Variant	rs6719831
Chromosome Location	chr2:96502590-96502591
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1043092	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11683523	0.91[CEU][hapmap]
rs11687113	0.82[CEU][hapmap]
rs11689832	0.91[CEU][hapmap]
rs11691090	0.82[EUR][1000 genomes]
rs11695514	0.86[CEU][hapmap]
rs12471991	0.84[EUR][1000 genomes]
rs1974770	0.81[EUR][1000 genomes]
rs2315417	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2315421	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2438978	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs2462774	0.82[CEU][hapmap]
rs2579519	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs28856333	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34639392	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4062989	0.83[EUR][1000 genomes]
rs4063021	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4527246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4907282	0.80[AMR][1000 genomes]
rs4907288	0.83[CEU][hapmap]
rs56791141	0.82[EUR][1000 genomes]
rs60452119	0.85[EUR][1000 genomes]
rs61409777	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62153679	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62156932	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6706905	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6707583	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717101	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6740563	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS 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	43 gene(s)	inside rSNPs	diseases
2	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1003371	chr2:96326106-96684876	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv874662	chr2:96334397-96578621	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv874664	chr2:96370571-96534132	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv874665	chr2:96370571-96596515	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv874666	chr2:96370571-96691125	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1004482	chr2:96408987-96596717	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv834303	chr2:96432935-96551704	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv428054	chr2:96438238-96627125	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv961832	chr2:96453677-96671971	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv874667	chr2:96465201-96596515	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv874668	chr2:96465201-96600569	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv1826589	chr2:96468292-96583910	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv1826305	chr2:96468492-96583710	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
17	esv1848259	chr2:96477989-96583252	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv834304	chr2:96493545-96667472	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6719831	FAHD2CP	cis	Muscle Skeletal	GTEx
rs6719831	FAHD2CP	cis	Adipose Subcutaneous	GTEx
rs6719831	FAHD2CP	cis	lung	GTEx
rs6719831	GPAT2	cis	Muscle Skeletal	GTEx
rs6719831	ADRA2B	cis	Nerve Tibial	GTEx
rs6719831	ADRA2B	cis	Thyroid	GTEx
rs6719831	ASTL	cis	Esophagus Mucosa	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96493000-96506400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:96494000-96503800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:96494000-96504600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:96494200-96502600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:96494200-96502600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:96494200-96503200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:96494200-96517600	Weak transcription	HUVEC	blood vessel
8	chr2:96494400-96506200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:96494600-96515800	Weak transcription	Fetal Brain Male	brain
10	chr2:96494800-96506200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:96495000-96523200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:96495000-96532800	Weak transcription	HSMM	muscle
13	chr2:96495600-96502800	Strong transcription	Thymus	Thymus
14	chr2:96495600-96504000	Weak transcription	HepG2	liver
15	chr2:96495600-96504200	Weak transcription	Right Ventricle	heart
16	chr2:96495600-96515800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:96495800-96503800	Weak transcription	Stomach Mucosa	stomach
18	chr2:96496000-96502800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:96496000-96502800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:96496200-96502600	Weak transcription	Pancreas	Pancrea
21	chr2:96496400-96515600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:96496600-96505200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:96496600-96521200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:96496800-96504400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:96497000-96502800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:96497000-96504000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:96497000-96515800	Weak transcription	Fetal Lung	lung
28	chr2:96497000-96515800	Weak transcription	NHEK	skin
29	chr2:96497400-96521200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:96497800-96502600	Strong transcription	Fetal Brain Female	brain
31	chr2:96497800-96503400	Strong transcription	Dnd41	blood
32	chr2:96497800-96504200	Weak transcription	NHLF	lung
33	chr2:96497800-96515800	Weak transcription	HSMMtube	muscle
34	chr2:96498000-96502800	Strong transcription	Ovary	ovary
35	chr2:96498600-96502800	Weak transcription	Placenta	Placenta
36	chr2:96498600-96503200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:96499000-96502800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:96499000-96502800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:96499000-96502800	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:96499200-96502800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:96499200-96502800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
42	chr2:96499200-96502800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:96499200-96502800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:96499200-96502800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:96499200-96503200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:96499400-96502800	Strong transcription	Fetal Intestine Small	intestine
47	chr2:96499600-96502800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:96499600-96503000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:96499600-96503000	Strong transcription	Adipose Nuclei	Adipose
50	chr2:96499800-96502600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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