Variant report

Variant	rs4687999
Chromosome Location	chr3:119090467-119090468
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10934492	0.86[YRI][hapmap]
rs16829700	1.00[CHB][hapmap]
rs16829712	1.00[CHB][hapmap]
rs2717264	1.00[AMR][1000 genomes]
rs4687842	1.00[AMR][1000 genomes]
rs4687849	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687850	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688000	1.00[CHB][hapmap]
rs6803331	1.00[EUR][1000 genomes]
rs72960637	1.00[EUR][1000 genomes]
rs72960640	1.00[EUR][1000 genomes]
rs72960642	1.00[EUR][1000 genomes]
rs73854487	1.00[EUR][1000 genomes]
rs73854488	1.00[EUR][1000 genomes]
rs7646935	1.00[EUR][1000 genomes]
rs878808	1.00[CHB][hapmap]
rs9289128	1.00[CHB][hapmap]
rs9832224	1.00[CHB][hapmap]
rs9845965	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4687999	KLHL34	trans	lymphoblastoid	seeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119069400-119111400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:119072000-119109200	Weak transcription	Brain Substantia Nigra	brain
3	chr3:119072000-119133800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:119072200-119099200	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:119072200-119100600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:119072200-119101400	Weak transcription	HSMM	muscle
7	chr3:119072200-119109600	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:119072200-119114200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:119073000-119098000	Weak transcription	Thymus	Thymus
10	chr3:119073000-119101000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:119076400-119098800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:119076400-119101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:119076400-119102000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:119076400-119109200	Weak transcription	Colonic Mucosa	Colon
15	chr3:119076400-119109200	Weak transcription	Esophagus	oesophagus
16	chr3:119076600-119101400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:119078800-119111400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:119079000-119102000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:119079400-119109600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:119079800-119110000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:119080000-119145600	Weak transcription	Fetal Kidney	kidney
22	chr3:119080200-119093800	Weak transcription	GM12878-XiMat	blood
23	chr3:119081200-119099200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:119081200-119135600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:119081400-119114200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:119082800-119138000	Weak transcription	Small Intestine	intestine
27	chr3:119084000-119090600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:119084000-119095000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:119084200-119091000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:119084200-119091000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:119084600-119091000	Strong transcription	HUVEC	blood vessel
32	chr3:119085000-119091800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:119085000-119109200	Weak transcription	Pancreas	Pancrea
34	chr3:119085200-119139000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:119085800-119090800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:119086400-119110000	Weak transcription	Fetal Thymus	thymus
37	chr3:119087400-119093000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:119087400-119093000	Weak transcription	Fetal Lung	lung
39	chr3:119087400-119093000	Weak transcription	Placenta	Placenta
40	chr3:119087400-119101200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:119087400-119101800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:119087800-119099800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:119087800-119101000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:119087800-119101800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:119088000-119093000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:119088000-119093400	Weak transcription	Right Ventricle	heart
47	chr3:119088000-119097400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:119088000-119098600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:119088000-119100000	Weak transcription	HSMMtube	muscle
50	chr3:119088000-119101200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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