Variant report

Variant	rs6993494
Chromosome Location	chr8:8667444-8667445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:8667410..8669876-chr8:8671325..8673532,2	K562	blood:
2	chr8:8665098..8666635-chr8:8667278..8670220,2	MCF-7	breast:
3	chr8:8663729..8665555-chr8:8666802..8669235,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10088933	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1039916	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs11783966	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12547493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12677550	0.88[CEU][hapmap];0.81[CHD][hapmap]
rs12682352	0.81[CHD][hapmap]
rs13254903	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs13260419	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13265731	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473029	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175161	0.91[AFR][1000 genomes]
rs2409090	0.93[YRI][hapmap]
rs28399241	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs332039	0.83[JPT][hapmap]
rs3748144	0.90[YRI][hapmap]
rs437895	0.88[CEU][hapmap]
rs4382480	0.83[JPT][hapmap]
rs440788	0.86[CEU][hapmap]
rs4841043	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4841044	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4841047	0.87[EUR][1000 genomes]
rs4841051	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs4841055	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs6601265	0.88[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs6988939	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7006589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7813355	0.84[CEU][hapmap]
rs7820324	0.84[CEU][hapmap]
rs7832968	0.92[CHB][hapmap]
rs9329167	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS 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	9 gene(s)	inside rSNPs	diseases
9	esv1824870	chr8:8583943-8699382	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv831228	chr8:8608387-8790790	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv1018828	chr8:8609880-8790660	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv1022331	chr8:8610035-8787981	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6993494	CTSB	cis	cerebellum	SCAN
rs6993494	FLJ10661	cis	cerebellum	SCAN
rs6993494	SGK223	cis	Thyroid	GTEx
rs6993494	MFHAS1	cis	cerebellum	SCAN
rs6993494	PRSS55	cis	cerebellum	SCAN
rs6993494	TDH	cis	cerebellum	SCAN
rs6993494	MFHAS1	cis	parietal	SCAN
rs6993494	C8orf5	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8637600-8679800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:8653800-8674800	Weak transcription	Brain Germinal Matrix	brain
3	chr8:8654000-8671000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:8655200-8680600	Weak transcription	Colonic Mucosa	Colon
5	chr8:8655600-8673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:8655600-8685600	Weak transcription	Fetal Brain Female	brain
7	chr8:8655800-8669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr8:8655800-8669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr8:8655800-8669200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr8:8655800-8669200	Weak transcription	Thymus	Thymus
11	chr8:8656000-8669600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr8:8656200-8669000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr8:8656200-8669000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr8:8658200-8668800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr8:8658200-8669000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:8658400-8669200	Weak transcription	Fetal Intestine Large	intestine
17	chr8:8658400-8675200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr8:8658400-8687200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr8:8659400-8671600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr8:8660200-8684400	Weak transcription	HSMMtube	muscle
21	chr8:8660600-8669000	Weak transcription	Dnd41	blood
22	chr8:8662200-8668200	Weak transcription	Primary T cells from cord blood	blood
23	chr8:8662400-8668400	Weak transcription	Fetal Intestine Small	intestine
24	chr8:8662600-8683400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr8:8662800-8679800	Weak transcription	Brain Angular Gyrus	brain
26	chr8:8663400-8691800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr8:8663600-8668000	Enhancers	Fetal Heart	heart
28	chr8:8663600-8681400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr8:8663800-8667600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr8:8663800-8669000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr8:8664000-8669200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr8:8664000-8669200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr8:8664000-8669200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr8:8664000-8673600	Weak transcription	Stomach Mucosa	stomach
35	chr8:8664000-8678600	Weak transcription	Spleen	Spleen
36	chr8:8664000-8682400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr8:8664200-8668000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr8:8664200-8669200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr8:8664200-8675000	Weak transcription	Hela-S3	cervix
40	chr8:8664200-8681200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:8664200-8691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr8:8664400-8668200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr8:8664400-8668400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr8:8664400-8675200	Weak transcription	Pancreas	Pancrea
45	chr8:8664400-8691800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr8:8664600-8683200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr8:8665000-8669200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr8:8665000-8670000	Enhancers	Fetal Lung	lung
49	chr8:8665200-8667600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr8:8665200-8668400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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