Variant report

Variant	rs4253342
Chromosome Location	chr4:187155809-187155810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs2089873	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34331648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35617964	1.00[EUR][1000 genomes]
rs4253335	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253340	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253341	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253344	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253351	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253353	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253355	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253356	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4253811	1.00[YRI][hapmap]
rs4253847	1.00[EUR][1000 genomes]
rs56960412	1.00[EUR][1000 genomes]
rs57684220	1.00[EUR][1000 genomes]
rs5967	1.00[EUR][1000 genomes]
rs60088731	1.00[EUR][1000 genomes]
rs67247234	1.00[EUR][1000 genomes]
rs6815582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6818265	1.00[EUR][1000 genomes]
rs6831571	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6831878	0.82[AFR][1000 genomes]
rs6834168	1.00[EUR][1000 genomes]
rs6846865	1.00[EUR][1000 genomes]
rs6852500	1.00[EUR][1000 genomes]
rs72646243	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72646252	1.00[EUR][1000 genomes]
rs72646264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72646268	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73025939	1.00[EUR][1000 genomes]
rs73025940	1.00[EUR][1000 genomes]
rs73025946	1.00[EUR][1000 genomes]
rs73025950	1.00[EUR][1000 genomes]
rs73025953	1.00[EUR][1000 genomes]
rs73025956	1.00[EUR][1000 genomes]
rs73025959	1.00[EUR][1000 genomes]
rs73025960	1.00[EUR][1000 genomes]
rs73025964	1.00[EUR][1000 genomes]
rs73025996	1.00[EUR][1000 genomes]
rs73027926	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73027987	1.00[EUR][1000 genomes]
rs73027999	1.00[EUR][1000 genomes]
rs73029819	1.00[EUR][1000 genomes]
rs73873787	1.00[EUR][1000 genomes]
rs749055	1.00[EUR][1000 genomes]
rs7669220	0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7669366	1.00[EUR][1000 genomes]
rs7682106	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
3	nsv931977	chr4:186912987-187364756	Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv869299	chr4:186958290-187192748	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1033203	chr4:186990348-187333476	Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv537431	chr4:186990348-187333476	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv461864	chr4:187006806-187257004	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv596392	chr4:187006806-187257004	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv830172	chr4:187012765-187168424	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv461865	chr4:187072383-187366649	Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
11	nsv596401	chr4:187072383-187366649	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv1022059	chr4:187082701-187183953	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv881231	chr4:187136307-187157458	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv881472	chr4:187152142-187187005	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187131800-187159000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr4:187131800-187181600	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:187146400-187172800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:187147800-187162000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:187148000-187161600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:187148000-187173000	Weak transcription	Psoas Muscle	Psoas
7	chr4:187148200-187159400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:187148200-187179200	Weak transcription	Lung	lung
9	chr4:187148400-187162000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:187148400-187164600	Weak transcription	Right Ventricle	heart
11	chr4:187148400-187172600	Weak transcription	Brain Anterior Caudate	brain
12	chr4:187148400-187179400	Weak transcription	Pancreas	Pancrea
13	chr4:187149600-187159400	Weak transcription	Fetal Intestine Small	intestine
14	chr4:187149800-187181600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:187149800-187186800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:187150000-187161000	Weak transcription	Aorta	Aorta
17	chr4:187150000-187162000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:187150200-187187200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:187151000-187187200	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:187151200-187161200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:187151800-187173000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr4:187152000-187179400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:187152200-187169800	Weak transcription	Brain Substantia Nigra	brain
24	chr4:187153000-187156800	Genic enhancers	Liver	Liver
25	chr4:187154000-187182000	Weak transcription	Primary T cells from cord blood	blood

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