Variant report

Variant	rs39502
Chromosome Location	chr8:90776812-90776813
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90774651..90777545-chr8:90807253..90809374,2	MCF-7	breast:
2	chr8:90775245..90777466-chr8:90780625..90782442,2	K562	blood:
3	chr8:90775597..90777487-chr8:90778142..90780568,2	K562	blood:
4	chr8:90776459..90778873-chr8:90786925..90789865,2	K562	blood:
5	chr8:90774118..90777411-chr8:90913721..90915849,3	MCF-7	breast:
6	chr8:90775966..90778463-chr8:90780267..90782442,2	K562	blood:

Variant related genes	Relation type
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12156013	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13254219	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13274635	0.89[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13276910	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs218904	0.83[CHD][hapmap]
rs218935	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs218938	0.89[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs369771	0.82[CEU][hapmap]
rs383592	0.82[CEU][hapmap]
rs394108	0.82[CEU][hapmap]
rs39501	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39508	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs39509	0.82[CEU][hapmap]
rs39510	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs39511	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs39512	0.86[EUR][1000 genomes]
rs39515	0.82[CEU][hapmap]
rs397540	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs39762	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39763	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs39765	0.83[CHD][hapmap];0.93[GIH][hapmap]
rs39766	0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs398701	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40248	0.83[EUR][1000 genomes]
rs40378	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40379	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40380	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs40454	0.85[CEU][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs40635	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs406680	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs411310	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs416324	0.82[CEU][hapmap]
rs42343	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs42479	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42480	0.89[CEU][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs425721	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs426779	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs428484	0.89[CEU][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs43133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434264	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs450332	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs51331	0.82[CEU][hapmap]
rs7815039	0.87[EUR][1000 genomes];0.89[ASN][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	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv891181	chr8:90737258-90819998	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs39502	CALB1	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90771000-90797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:90771600-90803800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:90771800-90777400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr8:90771800-90784400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr8:90771800-90805000	Weak transcription	Esophagus	oesophagus
6	chr8:90772000-90777400	Weak transcription	Primary T cells from cord blood	blood
7	chr8:90772000-90778000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr8:90772000-90778400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr8:90772000-90784600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr8:90772000-90785000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr8:90772000-90785400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:90772000-90796800	Weak transcription	Lung	lung
13	chr8:90772000-90797000	Weak transcription	Ovary	ovary
14	chr8:90772200-90777600	Weak transcription	Placenta	Placenta
15	chr8:90772200-90778000	Weak transcription	Fetal Kidney	kidney
16	chr8:90772200-90778200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr8:90772200-90778200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr8:90772200-90778200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr8:90772200-90783600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr8:90772200-90783800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr8:90772200-90784600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr8:90772200-90785200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr8:90772200-90785600	Weak transcription	Fetal Muscle Leg	muscle
24	chr8:90772200-90802000	Weak transcription	Colonic Mucosa	Colon
25	chr8:90772200-90802400	Weak transcription	Spleen	Spleen
26	chr8:90772200-90805200	Weak transcription	Fetal Brain Male	brain
27	chr8:90772200-90807200	Weak transcription	Pancreas	Pancrea
28	chr8:90772200-90809400	Weak transcription	Small Intestine	intestine
29	chr8:90772400-90777600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr8:90772400-90777600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr8:90772400-90778200	Weak transcription	Fetal Intestine Large	intestine
32	chr8:90772400-90778200	Weak transcription	Fetal Lung	lung
33	chr8:90772400-90784000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr8:90772400-90784600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr8:90772400-90784800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr8:90772400-90784800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr8:90772400-90785200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:90772400-90787200	Weak transcription	Fetal Stomach	stomach
39	chr8:90772400-90790600	Weak transcription	NHEK	skin
40	chr8:90772400-90802200	Weak transcription	Colon Smooth Muscle	Colon
41	chr8:90772600-90777800	Weak transcription	Liver	Liver
42	chr8:90772600-90784400	Weak transcription	Left Ventricle	heart
43	chr8:90773000-90783400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr8:90773000-90784400	Weak transcription	HSMMtube	muscle
45	chr8:90773000-90785200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr8:90773000-90785200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr8:90773000-90806800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr8:90773000-90812400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr8:90773200-90777400	Weak transcription	HUVEC	blood vessel
50	chr8:90773200-90777800	Weak transcription	Primary B cells from peripheral blood	blood

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