Variant report

Variant	rs11710016
Chromosome Location	chr3:101120030-101120031
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11707689	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11708616	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11711808	0.93[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs12638137	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12638796	0.93[EUR][1000 genomes]
rs17345528	0.86[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs17402964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2460723	0.81[JPT][hapmap]
rs348867	0.81[JPT][hapmap]
rs348877	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs348878	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs348882	0.81[JPT][hapmap]
rs348883	0.81[JPT][hapmap]
rs3762729	0.90[CEU][hapmap]
rs3804775	0.91[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs3804778	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap]
rs488679	0.81[JPT][hapmap]
rs518813	0.81[JPT][hapmap]
rs55710435	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56171035	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57880921	0.93[EUR][1000 genomes]
rs58835747	0.87[EUR][1000 genomes]
rs59359251	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6791964	0.82[EUR][1000 genomes]
rs72940399	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72942211	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72944107	0.93[EUR][1000 genomes]
rs72946021	0.83[EUR][1000 genomes]
rs7613046	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7641261	0.90[CEU][hapmap]
rs997739	0.91[CEU][hapmap];0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11710016	NIT2	cis	parietal	SCAN
rs11710016	SENP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101085600-101137600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:101106800-101133000	Weak transcription	Left Ventricle	heart
3	chr3:101106800-101133000	Weak transcription	Pancreas	Pancrea
4	chr3:101106800-101133000	Weak transcription	Spleen	Spleen
5	chr3:101107000-101140800	Weak transcription	Esophagus	oesophagus
6	chr3:101107200-101133000	Weak transcription	Gastric	stomach
7	chr3:101107200-101133000	Weak transcription	Thymus	Thymus
8	chr3:101107200-101161200	Weak transcription	Aorta	Aorta
9	chr3:101108600-101138000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:101109400-101133600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:101109800-101127000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:101110400-101123800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:101110600-101124000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:101110800-101132400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:101111600-101138000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:101111600-101145800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:101111800-101123800	Weak transcription	Lung	lung
18	chr3:101111800-101134800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:101112000-101125400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:101112600-101121800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:101113800-101121000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:101113800-101121800	Weak transcription	Fetal Intestine Large	intestine
23	chr3:101114000-101121000	Weak transcription	Adipose Nuclei	Adipose
24	chr3:101114200-101122000	Strong transcription	Primary T cells from cord blood	blood
25	chr3:101114600-101121800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:101114600-101123800	Weak transcription	Psoas Muscle	Psoas
27	chr3:101114600-101126000	Weak transcription	Fetal Brain Female	brain
28	chr3:101114600-101133000	Weak transcription	Fetal Thymus	thymus
29	chr3:101114600-101134800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:101114800-101121200	Strong transcription	Primary B cells from cord blood	blood
31	chr3:101114800-101122000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:101115000-101123600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:101115000-101126000	Weak transcription	Fetal Lung	lung
34	chr3:101115200-101121800	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:101115200-101133000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:101115600-101121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:101116200-101126200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:101116400-101123400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:101116400-101124000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:101116600-101125600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:101117000-101125200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:101117000-101127200	Weak transcription	Dnd41	blood
43	chr3:101117000-101129200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:101117000-101132800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:101117600-101130800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:101117800-101121800	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:101118000-101133000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:101118800-101121600	Weak transcription	Right Ventricle	heart
49	chr3:101119400-101120600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr3:101119400-101120800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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