Variant report

Variant	rs12465398
Chromosome Location	chr2:113009021-113009022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113008666..113014085-chr2:113030385..113035561,7	MCF-7	breast:
2	chr2:112995119..113002036-chr2:113006971..113012595,10	K562	blood:
3	chr2:112640166..112643875-chr2:113008551..113014158,5	K562	blood:
4	chr2:113006375..113009126-chr2:113033246..113034837,2	K562	blood:
5	chr2:113008180..113009810-chr2:113032329..113034455,2	K562	blood:
6	chr2:112998287..113000256-chr2:113007615..113010279,2	K562	blood:

Variant related genes	Relation type
ENSG00000144161	Chromatin interaction
ENSG00000153107	Chromatin interaction
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11898975	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11900089	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11900153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614282	0.94[ASN][1000 genomes]
rs12622246	0.94[ASN][1000 genomes]
rs12623743	0.84[ASN][1000 genomes]
rs13001618	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs13031326	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs2254860	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2312459	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35502956	0.98[ASN][1000 genomes]
rs7557904	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12465398	IL1F7	cis	parietal	SCAN
rs12465398	FBLN7	cis	parietal	SCAN
rs12465398	RGPD8	cis	Adipose Subcutaneous	GTEx
rs12465398	RGPD8	cis	Artery Tibial	GTEx
rs12465398	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs12465398	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs12465398	LOC653596	cis	multi-tissue	Pritchard
rs12465398	RGPD8	cis	lung	GTEx
rs12465398	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs12465398	RGPD8	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112968000-113011800	Weak transcription	Right Ventricle	heart
2	chr2:112968200-113009200	Weak transcription	Small Intestine	intestine
3	chr2:112968200-113012000	Weak transcription	Pancreas	Pancrea
4	chr2:112968800-113011400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:112968800-113011800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:112969400-113011800	Weak transcription	Esophagus	oesophagus
7	chr2:112970800-113011600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:112971400-113011600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:112971800-113011800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:112979600-113011600	Weak transcription	Fetal Kidney	kidney
11	chr2:112979600-113012000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:112980000-113011800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:112980200-113011600	Weak transcription	HSMM	muscle
14	chr2:112987200-113010800	Weak transcription	NH-A	brain
15	chr2:112987200-113011000	Weak transcription	NHDF-Ad	bronchial
16	chr2:112987400-113011400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:112987800-113011000	Weak transcription	NHEK	skin
18	chr2:112987800-113011800	Weak transcription	NHLF	lung
19	chr2:112988400-113011600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:112990800-113009200	Weak transcription	Hela-S3	cervix
21	chr2:112992200-113011400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:112992200-113011800	Weak transcription	HSMMtube	muscle
23	chr2:112993000-113011000	Weak transcription	HMEC	breast
24	chr2:112993400-113011000	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:112994600-113011800	Weak transcription	Colonic Mucosa	Colon
26	chr2:113000800-113009400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:113000800-113009600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:113001200-113011400	Weak transcription	HUVEC	blood vessel
29	chr2:113004000-113009800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:113004200-113009200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:113004200-113010200	Weak transcription	Fetal Brain Male	brain
32	chr2:113004200-113011400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:113004400-113011400	Weak transcription	Fetal Heart	heart
34	chr2:113004400-113011600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:113004400-113011800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:113004400-113012000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:113004600-113011400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:113005200-113011400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:113005600-113011000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:113005600-113011400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:113005600-113011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:113005600-113011400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:113005600-113011400	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:113005600-113011600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:113005800-113011000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:113005800-113011400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:113005800-113011800	Weak transcription	Aorta	Aorta
48	chr2:113005800-113011800	Weak transcription	Left Ventricle	heart
49	chr2:113005800-113012000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:113006600-113011000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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