Variant report

Variant	rs2315421
Chromosome Location	chr2:96497516-96497517
allele	A/C/G
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];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11683523	0.91[CEU][hapmap]
rs11687113	0.81[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];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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	0.83[CEU][hapmap]
rs2579519	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs28856333	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34639392	0.95[AFR][1000 genomes];0.96[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];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4527246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4907282	0.81[AMR][1000 genomes]
rs4907288	0.82[CEU][hapmap]
rs56791141	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60452119	0.85[EUR][1000 genomes]
rs61409777	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62153679	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62156932	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6706905	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707583	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6717101	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719831	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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
rs2315421	FAHD2CP	cis	lung	GTEx
rs2315421	FAHD2CP	cis	Adipose Subcutaneous	GTEx
rs2315421	ADRA2B	cis	Thyroid	GTEx
rs2315421	GPAT2	cis	Muscle Skeletal	GTEx
rs2315421	ASTL	cis	Esophagus Mucosa	GTEx
rs2315421	ADRA2B	cis	Nerve Tibial	GTEx
rs2315421	FAHD2CP	cis	Muscle Skeletal	GTEx

Chromatin state (count:82 , 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	chr2:96493200-96498000	Weak transcription	Fetal Kidney	kidney
3	chr2:96493200-96502000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:96493800-96499000	Weak transcription	Colonic Mucosa	Colon
5	chr2:96494000-96497800	ZNF genes & repeats	Dnd41	blood
6	chr2:96494000-96503800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:96494000-96504600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:96494200-96500400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:96494200-96501000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:96494200-96501400	ZNF genes & repeats	Fetal Stomach	stomach
11	chr2:96494200-96502000	Weak transcription	Brain Substantia Nigra	brain
12	chr2:96494200-96502600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:96494200-96502600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:96494200-96503200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:96494200-96517600	Weak transcription	HUVEC	blood vessel
16	chr2:96494400-96497800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:96494400-96499400	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr2:96494400-96501000	Strong transcription	Stomach Smooth Muscle	stomach
19	chr2:96494400-96506200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:96494600-96515800	Weak transcription	Fetal Brain Male	brain
21	chr2:96494800-96499200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:96494800-96502000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:96494800-96506200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:96495000-96498200	Strong transcription	Brain Germinal Matrix	brain
25	chr2:96495000-96523200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:96495000-96532800	Weak transcription	HSMM	muscle
27	chr2:96495200-96501800	Weak transcription	Small Intestine	intestine
28	chr2:96495200-96502400	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:96495400-96502400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:96495600-96502800	Strong transcription	Thymus	Thymus
31	chr2:96495600-96504000	Weak transcription	HepG2	liver
32	chr2:96495600-96504200	Weak transcription	Right Ventricle	heart
33	chr2:96495600-96515800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:96495800-96498200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr2:96495800-96499200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:96495800-96499200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:96495800-96503800	Weak transcription	Stomach Mucosa	stomach
38	chr2:96496000-96499600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:96496000-96502800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:96496000-96502800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:96496200-96499000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:96496200-96499400	Weak transcription	Brain Angular Gyrus	brain
43	chr2:96496200-96499400	Weak transcription	Spleen	Spleen
44	chr2:96496200-96500000	Weak transcription	Gastric	stomach
45	chr2:96496200-96500400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:96496200-96500400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:96496200-96502600	Weak transcription	Pancreas	Pancrea
48	chr2:96496400-96497800	ZNF genes & repeats	A549	lung
49	chr2:96496400-96499000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:96496400-96499200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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