Variant report

Variant	rs10899378
Chromosome Location	chr11:77166652-77166653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10899376	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899379	0.97[EUR][1000 genomes]
rs11237173	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11237189	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237193	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237195	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237196	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237199	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12271542	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1377470	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1377471	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453343	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17135625	0.86[ASN][1000 genomes]
rs1840151	0.97[EUR][1000 genomes]
rs2250639	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250647	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2298793	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602458	0.97[EUR][1000 genomes]
rs2602459	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602463	0.84[EUR][1000 genomes]
rs2602464	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602465	0.93[EUR][1000 genomes]
rs2602468	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602469	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602470	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602472	0.93[EUR][1000 genomes]
rs2602477	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602479	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602488	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2602489	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2725810	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2725815	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2725816	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2725826	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2725827	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2725830	0.97[EUR][1000 genomes]
rs2725831	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2725832	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2729747	0.93[EUR][1000 genomes]
rs2729753	0.81[EUR][1000 genomes]
rs2729762	0.87[EUR][1000 genomes]
rs2729769	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729771	0.84[EUR][1000 genomes]
rs2844328	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844332	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844333	0.87[EUR][1000 genomes]
rs2844334	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844336	0.86[EUR][1000 genomes]
rs2844337	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2852384	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852385	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2852392	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852394	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853086	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2853087	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853088	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2853090	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2853103	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3018424	0.80[ASN][1000 genomes]
rs4590893	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57111053	0.81[AFR][1000 genomes]
rs59348236	0.83[AFR][1000 genomes]
rs7109645	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7119033	0.95[EUR][1000 genomes]
rs7943778	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77153600-77168600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:77155400-77181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:77157000-77168400	Weak transcription	Small Intestine	intestine
4	chr11:77158200-77168600	Weak transcription	Stomach Mucosa	stomach
5	chr11:77158400-77169800	Weak transcription	Fetal Intestine Large	intestine
6	chr11:77159800-77168400	Weak transcription	Fetal Brain Female	brain
7	chr11:77160200-77169400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:77160600-77178000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:77160800-77167000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:77161000-77170200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:77161200-77167400	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:77161200-77179200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr11:77162400-77166800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:77162400-77167000	Weak transcription	Primary B cells from cord blood	blood
15	chr11:77162400-77167200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:77162400-77167400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:77162400-77168000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr11:77163000-77173400	Weak transcription	Placenta	Placenta
19	chr11:77164000-77169800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:77165000-77168200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr11:77165000-77172200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:77165200-77166800	Weak transcription	Fetal Intestine Small	intestine
23	chr11:77165200-77166800	Enhancers	GM12878-XiMat	blood
24	chr11:77165200-77170800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:77165400-77168200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr11:77165600-77167000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:77165600-77168200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr11:77165600-77168200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr11:77165800-77168600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr11:77165800-77171200	Enhancers	H1 Cell Line	embryonic stem cell
31	chr11:77166000-77167600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr11:77166000-77167800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:77166000-77168400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr11:77166200-77167600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr11:77166200-77172800	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr11:77166400-77166800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr11:77166400-77167000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:77166600-77168400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr11:77166600-77168400	Weak transcription	Brain Germinal Matrix	brain
40	chr11:77166600-77168400	Weak transcription	Psoas Muscle	Psoas

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