Variant report

Variant	rs793475
Chromosome Location	chr3:99543764-99543765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99535807..99538433-chr3:99542734..99545509,2	MCF-7	breast:
2	chr3:99542264..99544347-chr3:99597790..99600681,3	K562	blood:
3	chr3:99542625..99544746-chr3:99551847..99553962,2	K562	blood:
4	chr3:99534858..99539384-chr3:99540640..99546011,10	K562	blood:
5	chr3:99543572..99547778-chr3:99548143..99551852,5	K562	blood:
6	chr3:99543572..99545458-chr3:99547797..99549652,2	K562	blood:

Variant related genes	Relation type
ENSG00000184220	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11719468	0.84[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1287284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13059754	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1384062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1610509	0.84[JPT][hapmap]
rs16841874	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs1718235	0.84[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2638948	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35422475	0.84[AMR][1000 genomes]
rs4577503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928150	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928230	0.83[CEU][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4928235	0.83[AMR][1000 genomes]
rs4928237	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes]
rs6440967	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6806323	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs704571	0.85[JPT][hapmap]
rs704572	0.90[JPT][hapmap]
rs704574	0.84[JPT][hapmap]
rs7613864	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7649349	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs7650727	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs792831	0.85[JPT][hapmap]
rs792835	0.84[JPT][hapmap]
rs792836	0.85[JPT][hapmap]
rs792837	0.85[JPT][hapmap]
rs793437	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs793443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793446	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793456	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793476	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793483	0.84[JPT][hapmap]
rs793485	0.85[JPT][hapmap]
rs793497	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793502	0.82[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs796976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs813218	0.83[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs902159	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs793475	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99562600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
3	chr3:99537400-99544200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:99537400-99551000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:99537400-99552400	Weak transcription	Ovary	ovary
6	chr3:99537800-99544400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:99537800-99547600	Weak transcription	Aorta	Aorta
8	chr3:99537800-99548200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:99537800-99552400	Weak transcription	Pancreas	Pancrea
10	chr3:99537800-99561800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:99537800-99562400	Weak transcription	Left Ventricle	heart
12	chr3:99538000-99543800	Weak transcription	A549	lung
13	chr3:99538000-99543800	Weak transcription	HSMM	muscle
14	chr3:99538000-99543800	Weak transcription	NH-A	brain
15	chr3:99538000-99544000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:99538000-99544000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:99538000-99544000	Weak transcription	NHDF-Ad	bronchial
18	chr3:99538000-99544000	Weak transcription	Osteobl	bone
19	chr3:99538000-99550400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:99538000-99550800	Weak transcription	Brain Anterior Caudate	brain
21	chr3:99538000-99552000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:99538000-99552400	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:99538000-99556000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:99538000-99556800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:99538000-99563600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:99538200-99543800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:99538200-99544000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:99538200-99544000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:99538200-99544000	Weak transcription	HMEC	breast
30	chr3:99538200-99544400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:99538200-99547200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:99538200-99550800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:99538200-99555400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
35	chr3:99538400-99543800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:99538400-99544600	Weak transcription	Adipose Nuclei	Adipose
37	chr3:99538400-99550800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:99538400-99551000	Weak transcription	Primary B cells from cord blood	blood
39	chr3:99538600-99544000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:99540200-99543800	Weak transcription	Hela-S3	cervix
41	chr3:99540200-99550600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:99540400-99544000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:99540400-99544000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:99540800-99552000	Weak transcription	GM12878-XiMat	blood
45	chr3:99541200-99550400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:99542200-99543800	Enhancers	K562	blood
47	chr3:99542400-99544000	Enhancers	HUVEC	blood vessel
48	chr3:99542800-99544200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:99542800-99548200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:99542800-99548400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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