Variant report

Variant	rs4848343
Chromosome Location	chr2:114491636-114491637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:114490228..114492803-chr2:114497199..114499336,2	K562	blood:
2	chr2:114485598..114489125-chr2:114489448..114492903,4	MCF-7	breast:
3	chr2:114489220..114494215-chr2:114513189..114517576,5	K562	blood:
4	chr2:114482159..114484951-chr2:114491076..114492999,2	MCF-7	breast:
5	chr2:114489926..114491643-chr2:114503029..114505332,2	K562	blood:
6	chr2:114490228..114492106-chr2:114494949..114498699,3	K562	blood:
7	chr2:114491572..114494215-chr2:114513189..114515373,3	K562	blood:

Variant related genes	Relation type
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10167730	0.89[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10172842	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10177576	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10179657	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10209098	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12711788	0.82[EUR][1000 genomes]
rs1375332	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2122097	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2290108	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305255	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442136	0.89[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2595152	0.89[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap]
rs2687627	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28451366	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2900744	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36062527	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3816384	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3890789	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4848345	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4848349	0.81[EUR][1000 genomes]
rs4849270	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849277	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4849279	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6711542	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7560480	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7577893	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7600228	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4848343	RPL23AP7	cis	Esophagus Muscularis	GTEx
rs4848343	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs4848343	RPL23AP7	cis	Whole Blood	GTEx
rs4848343	RPL23AP7	cis	Nerve Tibial	GTEx
rs4848343	RPL23AP7	cis	lung	GTEx
rs4848343	RPL23AP7	cis	Muscle Skeletal	GTEx
rs4848343	DDX11L2	cis	Whole Blood	GTEx
rs4848343	RPL23AP7	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:114458400-114497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:114458400-114500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
5	chr2:114461600-114499800	Weak transcription	Hela-S3	cervix
6	chr2:114462000-114497400	Weak transcription	Colonic Mucosa	Colon
7	chr2:114463000-114498800	Weak transcription	Esophagus	oesophagus
8	chr2:114464000-114497600	Weak transcription	Right Ventricle	heart
9	chr2:114464000-114497600	Weak transcription	Spleen	Spleen
10	chr2:114465200-114512000	Weak transcription	Stomach Mucosa	stomach
11	chr2:114467400-114497200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:114469400-114510400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:114470000-114497400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:114470000-114500200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:114470200-114493400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:114470200-114511200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:114470400-114510800	Strong transcription	HSMM	muscle
19	chr2:114471000-114495600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:114471000-114495600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:114471000-114498600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:114471000-114500200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:114473200-114494600	Weak transcription	Fetal Heart	heart
24	chr2:114473800-114497200	Weak transcription	NHEK	skin
25	chr2:114474400-114494600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:114474400-114507600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:114476000-114506600	Weak transcription	Thymus	Thymus
28	chr2:114478800-114504400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:114478800-114507600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:114478800-114510600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:114479200-114510400	Strong transcription	Liver	Liver
32	chr2:114479800-114507000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:114480000-114492800	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:114480000-114504000	Strong transcription	Primary B cells from cord blood	blood
35	chr2:114480600-114494600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:114480600-114497400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:114480800-114497000	Weak transcription	HUVEC	blood vessel
38	chr2:114481200-114513000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:114482600-114493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:114482600-114493800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:114482600-114495000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:114483000-114506600	Weak transcription	Psoas Muscle	Psoas
43	chr2:114483600-114492400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:114484000-114493200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:114484000-114511200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:114484200-114493400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr2:114484400-114510600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:114484600-114497600	Weak transcription	Ovary	ovary
49	chr2:114484600-114512600	Weak transcription	Aorta	Aorta
50	chr2:114484800-114495000	Strong transcription	NHDF-Ad	bronchial

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