Variant report

Variant	rs10741725
Chromosome Location	chr11:17320797-17320798
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs214082	0.83[CHD][hapmap];0.88[LWK][hapmap];0.92[YRI][hapmap]
rs214083	0.96[YRI][hapmap]
rs214092	0.83[CHD][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap]
rs214093	0.92[YRI][hapmap]
rs214097	0.83[CHD][hapmap];0.89[LWK][hapmap];0.92[YRI][hapmap]
rs214106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs214914	0.82[CHB][hapmap]
rs7925692	0.82[ASW][hapmap]
rs7933137	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	esv1836937	chr11:17291499-17339127	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1799284	chr11:17299390-17343486	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1799280	chr11:17299390-17354775	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	esv1801731	chr11:17299390-17354775	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv897017	chr11:17318236-17343486	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10741725	Contig29193_RC	cis	multi-tissue	Pritchard
rs10741725	NUCB2	cis	cerebellum	SCAN
rs10741725	PDE3B	cis	parietal	SCAN
rs10741725	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs10741725	NUCB2	cis	Lymphoblastoid	GTEx
rs10741725	NUCB2	cis	lymphoblastoid	seeQTL
rs10741725	RP1-239B22.5	cis	Esophagus Mucosa	GTEx
rs10741725	KCNJ11	cis	multi-tissue	Pritchard
rs10741725	SPTY2D1	cis	parietal	SCAN
rs10741725	OR7E14P	cis	Esophagus Mucosa	GTEx
rs10741725	NUCB2	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17299000-17323200	Weak transcription	Ovary	ovary
2	chr11:17299000-17323400	Weak transcription	Aorta	Aorta
3	chr11:17299000-17357200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:17299000-17357600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:17299000-17360600	Weak transcription	Small Intestine	intestine
6	chr11:17299200-17325600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:17299200-17329600	Weak transcription	Brain Hippocampus Middle	brain
8	chr11:17299200-17357000	Weak transcription	Brain Substantia Nigra	brain
9	chr11:17299400-17338200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:17299400-17355400	Weak transcription	Brain Angular Gyrus	brain
11	chr11:17299400-17357000	Weak transcription	Fetal Intestine Large	intestine
12	chr11:17299600-17335000	Weak transcription	Primary B cells from cord blood	blood
13	chr11:17299800-17327600	Weak transcription	HUVEC	blood vessel
14	chr11:17300200-17335000	Weak transcription	Fetal Brain Male	brain
15	chr11:17301600-17350400	Weak transcription	Fetal Heart	heart
16	chr11:17302200-17321800	Weak transcription	NHEK	skin
17	chr11:17302600-17329600	Weak transcription	K562	blood
18	chr11:17305800-17332400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:17306200-17353000	Weak transcription	Colon Smooth Muscle	Colon
20	chr11:17307600-17328000	Weak transcription	Pancreas	Pancrea
21	chr11:17307800-17333600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:17308200-17323000	Weak transcription	Lung	lung
23	chr11:17308200-17335800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:17308200-17353600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr11:17308200-17357600	Weak transcription	HepG2	liver
26	chr11:17308200-17360800	Strong transcription	Fetal Thymus	thymus
27	chr11:17308200-17372600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:17308400-17335000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:17308400-17335000	Weak transcription	NHLF	lung
30	chr11:17308400-17356800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:17308400-17361600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:17308800-17331800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:17308800-17331800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:17309000-17324200	Weak transcription	Brain Germinal Matrix	brain
35	chr11:17309000-17327400	Weak transcription	Fetal Brain Female	brain
36	chr11:17309000-17331200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:17309000-17355600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:17309200-17323200	Weak transcription	Fetal Muscle Leg	muscle
39	chr11:17309400-17335200	Weak transcription	Psoas Muscle	Psoas
40	chr11:17309600-17329600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr11:17310800-17323400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:17311600-17321800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:17312200-17355400	Weak transcription	Fetal Kidney	kidney
44	chr11:17313800-17335400	Weak transcription	HSMMtube	muscle
45	chr11:17314200-17353400	Weak transcription	Stomach Mucosa	stomach
46	chr11:17314400-17335000	Strong transcription	Dnd41	blood
47	chr11:17315200-17335000	Weak transcription	Colonic Mucosa	Colon
48	chr11:17315400-17335000	Weak transcription	Spleen	Spleen
49	chr11:17315400-17353400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:17316000-17335200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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