Variant report

Variant	rs11600998
Chromosome Location	chr11:77452790-77452791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11237280	0.95[ASN][1000 genomes]
rs11603438	0.98[ASN][1000 genomes]
rs11604207	0.98[ASN][1000 genomes]
rs2508181	0.81[EUR][1000 genomes]
rs34130561	0.89[ASN][1000 genomes]
rs4344516	0.81[ASN][1000 genomes]
rs484363	0.89[ASN][1000 genomes]
rs56218634	0.95[ASN][1000 genomes]
rs621456	0.82[ASN][1000 genomes]
rs623173	0.82[ASN][1000 genomes]
rs643388	0.95[ASN][1000 genomes]
rs648896	0.82[ASN][1000 genomes]
rs668701	0.82[ASN][1000 genomes]
rs684813	0.89[ASN][1000 genomes]
rs72945598	0.98[ASN][1000 genomes]
rs72947625	0.98[ASN][1000 genomes]
rs72947668	1.00[ASN][1000 genomes]
rs72949616	0.95[ASN][1000 genomes]
rs72949618	0.95[ASN][1000 genomes]
rs7950873	0.86[ASN][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	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
2	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
3	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11600998	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77394600-77458800	Weak transcription	Small Intestine	intestine
2	chr11:77394800-77462600	Weak transcription	Fetal Heart	heart
3	chr11:77409600-77453400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:77409600-77458800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:77409600-77478200	Weak transcription	Brain Angular Gyrus	brain
6	chr11:77410400-77477600	Weak transcription	Brain Substantia Nigra	brain
7	chr11:77431600-77482400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:77436200-77458600	Weak transcription	HSMMtube	muscle
9	chr11:77436200-77462600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:77436200-77463000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:77436200-77473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:77436200-77477000	Weak transcription	Colonic Mucosa	Colon
13	chr11:77436600-77473200	Weak transcription	NHDF-Ad	bronchial
14	chr11:77436800-77458600	Weak transcription	NH-A	brain
15	chr11:77442000-77453000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:77442400-77458200	Weak transcription	Colon Smooth Muscle	Colon
17	chr11:77442400-77458400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:77442400-77458400	Weak transcription	NHEK	skin
19	chr11:77442400-77458600	Weak transcription	Psoas Muscle	Psoas
20	chr11:77442400-77458600	Weak transcription	HMEC	breast
21	chr11:77442400-77463600	Weak transcription	Brain Anterior Caudate	brain
22	chr11:77442400-77472600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:77442800-77474600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:77442800-77500200	Weak transcription	Pancreas	Pancrea
25	chr11:77443000-77465800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:77443200-77473600	Weak transcription	Fetal Brain Female	brain
27	chr11:77443200-77500200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:77443400-77458400	Weak transcription	A549	lung
29	chr11:77443400-77464400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:77443800-77454400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:77443800-77465800	Weak transcription	Brain Germinal Matrix	brain
32	chr11:77444200-77455600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:77444400-77453000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:77444800-77453000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr11:77445000-77458600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr11:77445400-77454400	Strong transcription	Primary hematopoietic stem cells	blood
37	chr11:77445400-77455800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr11:77445800-77476800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:77446000-77453000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:77446000-77465800	Weak transcription	Fetal Kidney	kidney
41	chr11:77446200-77458400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:77446200-77458800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr11:77446200-77461600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:77446200-77461800	Weak transcription	Gastric	stomach
45	chr11:77446200-77463200	Weak transcription	Aorta	Aorta
46	chr11:77446200-77463200	Weak transcription	Left Ventricle	heart
47	chr11:77446200-77464800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr11:77446200-77465800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:77446200-77467200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr11:77446200-77482400	Weak transcription	Spleen	Spleen

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