Variant report

Variant	rs11740800
Chromosome Location	chr5:52948984-52948985
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10513019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11738542	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740228	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11741008	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11749849	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16881514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16881524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16881561	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16881602	1.00[YRI][hapmap]
rs1847471	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2087618	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs28855127	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3958630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4147735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4147739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147742	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4549481	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4640749	0.87[ASN][1000 genomes]
rs55828101	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6872395	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6888501	1.00[YRI][hapmap]
rs6892641	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72750138	0.84[ASN][1000 genomes]
rs72750151	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72751832	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72751833	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72751838	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72751849	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72753647	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72753650	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72753658	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72753680	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72755395	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72757304	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72757372	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72757390	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7716949	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7729894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv880426	chr5:52885100-52953048	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	esv3394377	chr5:52945895-52949593	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52904400-52966600	Weak transcription	Osteobl	bone
2	chr5:52920800-52978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:52921600-52963400	Weak transcription	A549	lung
4	chr5:52925600-52961200	Weak transcription	Esophagus	oesophagus
5	chr5:52925800-52952000	Weak transcription	Colonic Mucosa	Colon
6	chr5:52926800-52963600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:52927400-52961000	Weak transcription	Placenta	Placenta
8	chr5:52927800-52961200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:52927800-52961200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:52927800-52961200	Weak transcription	Thymus	Thymus
11	chr5:52928000-52962200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:52929000-52981800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:52929400-52964600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:52933200-52951600	Weak transcription	Aorta	Aorta
15	chr5:52935200-52978000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:52937200-52963600	Weak transcription	NHLF	lung
17	chr5:52938200-52954800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:52938200-52970200	Weak transcription	NH-A	brain
19	chr5:52938400-52952400	Weak transcription	Small Intestine	intestine
20	chr5:52938400-52961000	Weak transcription	Fetal Stomach	stomach
21	chr5:52938400-52967600	Weak transcription	Fetal Kidney	kidney
22	chr5:52938600-52971000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:52939600-52960600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:52939800-52959600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:52940000-52982000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:52941200-52963400	Weak transcription	Hela-S3	cervix
27	chr5:52941400-52980200	Weak transcription	HepG2	liver
28	chr5:52941400-52985200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:52942400-52973400	Weak transcription	Fetal Heart	heart
30	chr5:52942600-52962200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:52943400-52961000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:52943400-52961600	Weak transcription	Fetal Intestine Large	intestine
33	chr5:52944000-52969800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:52944200-52968200	Weak transcription	K562	blood
35	chr5:52944600-52949000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:52944800-52955000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:52945200-52949000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:52945400-52951600	Weak transcription	Left Ventricle	heart
39	chr5:52945400-52954200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr5:52945400-52954600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:52945400-52954600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr5:52945400-52954800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:52945400-52954800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:52945400-52955200	Weak transcription	Dnd41	blood
45	chr5:52945400-52961000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:52945400-52961000	Weak transcription	Fetal Muscle Leg	muscle
47	chr5:52945400-52961200	Weak transcription	Adipose Nuclei	Adipose
48	chr5:52945400-52961200	Weak transcription	Ovary	ovary
49	chr5:52945400-52974600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr5:52945400-52979000	Weak transcription	HMEC	breast

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