Variant report

Variant	rs7777468
Chromosome Location	chr7:140071315-140071316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10281239	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11764502	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11771118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773054	0.82[EUR][1000 genomes]
rs28519439	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3924960	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59072471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60864294	1.00[EUR][1000 genomes]
rs6464705	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943032	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947516	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6955063	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6962376	0.97[EUR][1000 genomes]
rs6964259	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6966078	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6976631	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6978245	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73472784	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73472791	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7784544	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7788727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7789964	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806111	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9640465	0.82[EUR][1000 genomes]

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	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7777468	SLC37A3	cis	cerebellum	SCAN
rs7777468	SLC37A3	cis	parietal	SCAN
rs7777468	TBXAS1	cis	cerebellum	SCAN
rs7777468	EPHB6	cis	cerebellum	SCAN
rs7777468	OR9A4	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140033600-140096000	Weak transcription	Stomach Mucosa	stomach
2	chr7:140034800-140085600	Weak transcription	Psoas Muscle	Psoas
3	chr7:140035000-140074200	Weak transcription	Right Atrium	heart
4	chr7:140042000-140084800	Weak transcription	Hela-S3	cervix
5	chr7:140046000-140076200	Weak transcription	Right Ventricle	heart
6	chr7:140047600-140084200	Weak transcription	Fetal Brain Male	brain
7	chr7:140049200-140090200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:140049600-140076000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:140049600-140078000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:140049600-140078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:140049600-140079400	Weak transcription	Brain Substantia Nigra	brain
12	chr7:140050200-140079200	Weak transcription	HUVEC	blood vessel
13	chr7:140051600-140076400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr7:140052600-140075600	Weak transcription	Pancreas	Pancrea
16	chr7:140052800-140079600	Weak transcription	NHDF-Ad	bronchial
17	chr7:140054200-140079800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:140054600-140077800	Weak transcription	Brain Angular Gyrus	brain
19	chr7:140055000-140077800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr7:140055600-140079200	Weak transcription	Fetal Kidney	kidney
21	chr7:140056800-140077400	Weak transcription	NH-A	brain
22	chr7:140056800-140079400	Weak transcription	Colonic Mucosa	Colon
23	chr7:140057400-140075400	Weak transcription	Osteobl	bone
24	chr7:140058600-140075400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:140058600-140075600	Weak transcription	HepG2	liver
26	chr7:140058600-140077800	Weak transcription	Brain Hippocampus Middle	brain
27	chr7:140058600-140096000	Weak transcription	Small Intestine	intestine
28	chr7:140058800-140075600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr7:140058800-140075600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:140058800-140075600	Weak transcription	Aorta	Aorta
31	chr7:140058800-140077800	Weak transcription	Placenta	Placenta
32	chr7:140058800-140079200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr7:140058800-140081400	Weak transcription	A549	lung
34	chr7:140058800-140084400	Weak transcription	Gastric	stomach
35	chr7:140058800-140097200	Weak transcription	Brain Anterior Caudate	brain
36	chr7:140059400-140075400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:140059400-140091400	Weak transcription	Fetal Heart	heart
38	chr7:140059600-140075600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr7:140059600-140075600	Weak transcription	NHLF	lung
40	chr7:140060000-140075600	Weak transcription	GM12878-XiMat	blood
41	chr7:140060200-140075600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr7:140060800-140074400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:140061000-140075600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr7:140061000-140076200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:140063400-140082600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr7:140064600-140075200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr7:140064800-140075600	Weak transcription	Fetal Lung	lung
48	chr7:140065000-140075600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:140065000-140077000	Weak transcription	HMEC	breast
50	chr7:140065000-140077800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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