Variant report

Variant	rs11601940
Chromosome Location	chr11:9827871-9827872
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]
rs10500709	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11042505	0.81[AMR][1000 genomes]
rs11042521	1.00[ASN][1000 genomes]
rs11042525	1.00[ASN][1000 genomes]
rs11601125	1.00[ASN][1000 genomes]
rs11601212	1.00[ASN][1000 genomes]
rs11603291	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12416694	0.85[CEU][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12416904	1.00[ASN][1000 genomes]
rs12416993	1.00[ASN][1000 genomes]
rs12419046	1.00[ASN][1000 genomes]
rs12419471	1.00[ASN][1000 genomes]
rs17269812	1.00[ASN][1000 genomes]
rs55693083	1.00[ASN][1000 genomes]
rs55782221	1.00[ASN][1000 genomes]
rs61876873	1.00[ASN][1000 genomes]
rs61876881	1.00[ASN][1000 genomes]
rs61876891	1.00[ASN][1000 genomes]
rs61876893	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61876894	0.88[AMR][1000 genomes];1.00[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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS 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	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS 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	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
4	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11601940	SCUBE2	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9803200-9828600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:9803200-9828600	Weak transcription	Gastric	stomach
3	chr11:9803200-9828800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr11:9806800-9828600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr11:9808400-9828800	Weak transcription	Fetal Kidney	kidney
6	chr11:9809600-9828600	Weak transcription	Esophagus	oesophagus
7	chr11:9809600-9832600	Weak transcription	Colonic Mucosa	Colon
8	chr11:9809800-9828000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:9809800-9828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:9810000-9829200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr11:9810200-9828400	Weak transcription	Primary T cells from cord blood	blood
12	chr11:9810200-9829200	Weak transcription	Fetal Brain Male	brain
13	chr11:9810800-9828600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr11:9810800-9829000	Weak transcription	Right Ventricle	heart
15	chr11:9811000-9828600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:9811600-9828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:9811600-9828600	Weak transcription	Dnd41	blood
18	chr11:9811600-9828600	Weak transcription	HUVEC	blood vessel
19	chr11:9811600-9828800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:9811600-9828800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:9811800-9828400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr11:9811800-9828600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:9811800-9828800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:9811800-9828800	Weak transcription	Brain Germinal Matrix	brain
25	chr11:9811800-9828800	Weak transcription	Lung	lung
26	chr11:9811800-9828800	Weak transcription	Thymus	Thymus
27	chr11:9812000-9828400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:9812200-9862200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:9812400-9828400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:9818600-9881400	Weak transcription	Spleen	Spleen
31	chr11:9819200-9828000	Weak transcription	Primary B cells from cord blood	blood
32	chr11:9820000-9828600	Weak transcription	Pancreas	Pancrea
33	chr11:9820200-9828600	Weak transcription	Fetal Brain Female	brain
34	chr11:9820400-9828600	Weak transcription	Fetal Intestine Small	intestine
35	chr11:9821400-9828600	Weak transcription	Fetal Lung	lung
36	chr11:9821800-9830000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:9822400-9828000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:9824200-9837200	Weak transcription	Hela-S3	cervix
39	chr11:9824200-9867600	Weak transcription	Psoas Muscle	Psoas
40	chr11:9824400-9828600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr11:9824400-9828600	Weak transcription	Brain Substantia Nigra	brain
42	chr11:9824400-9828600	Weak transcription	HepG2	liver
43	chr11:9824400-9831800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:9824400-9841400	Weak transcription	Fetal Heart	heart
45	chr11:9824600-9828000	Weak transcription	Adipose Nuclei	Adipose
46	chr11:9824600-9828400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:9824600-9828600	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:9824600-9828800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:9824800-9831400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr11:9824800-9834400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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