Variant report

Variant	rs7702304
Chromosome Location	chr5:96032095-96032096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1037683	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11738135	0.85[AFR][1000 genomes]
rs12188168	0.86[AFR][1000 genomes]
rs12514686	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12518441	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17086521	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17086550	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17086588	0.81[ASW][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17086596	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs17086611	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs6862241	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6864233	0.81[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7718593	0.91[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7702304	CTD-2260A17.1	cis	lung	GTEx
rs7702304	MCTP1	cis	parietal	SCAN
rs7702304	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs7702304	CAST	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95999400-96038000	Weak transcription	Fetal Stomach	stomach
2	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung
4	chr5:96000800-96037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:96001600-96037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr5:96002400-96037600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:96002400-96038200	Weak transcription	Esophagus	oesophagus
8	chr5:96004800-96036600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:96005000-96038000	Weak transcription	Ovary	ovary
10	chr5:96005000-96038200	Weak transcription	Gastric	stomach
11	chr5:96009200-96037600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:96013000-96037800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:96013800-96037600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:96016600-96035200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:96016800-96035000	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:96016800-96038200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:96017000-96034000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:96017000-96038000	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:96018800-96038200	Weak transcription	Colonic Mucosa	Colon
20	chr5:96018800-96038200	Weak transcription	Spleen	Spleen
21	chr5:96022200-96034800	Weak transcription	NH-A	brain
22	chr5:96023000-96035000	Weak transcription	Right Ventricle	heart
23	chr5:96023000-96038400	Weak transcription	Small Intestine	intestine
24	chr5:96023200-96037600	Weak transcription	Thymus	Thymus
25	chr5:96023600-96033000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:96023600-96035000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:96023600-96036800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:96023800-96037000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:96023800-96037600	Weak transcription	Fetal Kidney	kidney
30	chr5:96023800-96038000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:96024000-96038200	Weak transcription	GM12878-XiMat	blood
32	chr5:96024800-96035200	Weak transcription	Brain Angular Gyrus	brain
33	chr5:96025600-96037200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:96026200-96037600	Weak transcription	Psoas Muscle	Psoas
35	chr5:96027200-96033400	Weak transcription	HUVEC	blood vessel
36	chr5:96027400-96035800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:96027800-96036200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr5:96028200-96033600	Weak transcription	K562	blood
39	chr5:96028400-96032600	Weak transcription	HMEC	breast
40	chr5:96028400-96033400	Weak transcription	Adipose Nuclei	Adipose
41	chr5:96028400-96034200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:96028400-96035000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:96028400-96037600	Weak transcription	Right Atrium	heart
44	chr5:96028400-96038200	Weak transcription	Lung	lung
45	chr5:96028400-96038600	Weak transcription	Aorta	Aorta
46	chr5:96028600-96033800	Weak transcription	NHDF-Ad	bronchial
47	chr5:96028600-96035000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:96028600-96035000	Weak transcription	NHLF	lung
49	chr5:96028800-96032600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr5:96028800-96035000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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