Variant report

Variant	rs10457074
Chromosome Location	chr6:149359829-149359830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149358004..149360292-chr6:149400901..149403577,2	MCF-7	breast:
2	chr6:149350394..149355236-chr6:149357019..149360236,5	K562	blood:
3	chr6:149351690..149353369-chr6:149357308..149360096,2	K562	blood:

Variant related genes	Relation type
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10872629	0.80[AMR][1000 genomes]
rs10872630	0.81[JPT][hapmap]
rs10872631	0.87[JPT][hapmap]
rs11755147	0.87[JPT][hapmap]
rs11759315	0.86[JPT][hapmap]
rs12201653	0.87[JPT][hapmap]
rs12211152	0.93[JPT][hapmap]
rs1317171	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1320575	0.86[ASN][1000 genomes]
rs17669693	0.87[JPT][hapmap]
rs17732007	0.87[JPT][hapmap]
rs1934220	0.87[JPT][hapmap]
rs1934224	0.86[CEU][hapmap]
rs2275423	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2340751	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2340752	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2340798	0.91[CEU][hapmap]
rs2340801	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2340802	0.91[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2879843	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4318907	0.95[CEU][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4377808	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4897074	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4897076	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4897078	0.87[JPT][hapmap]
rs6570920	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6570933	0.85[ASN][1000 genomes]
rs6570934	0.83[ASN][1000 genomes]
rs6570935	0.84[ASN][1000 genomes]
rs6901019	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6903827	0.87[JPT][hapmap]
rs6904550	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6915298	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6930989	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6931675	0.91[CEU][hapmap];0.90[CHB][hapmap];0.87[MEX][hapmap]
rs6931744	0.91[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6932386	0.87[JPT][hapmap]
rs6935330	0.83[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[ASN][1000 genomes]
rs6936176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939103	0.87[JPT][hapmap]
rs7738162	0.87[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs7747463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748978	0.81[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7756263	0.81[JPT][hapmap]
rs7760242	0.88[ASN][1000 genomes]
rs7761119	0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs7765778	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7772696	0.87[JPT][hapmap]
rs7774457	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7774887	0.95[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7776117	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9285516	0.87[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs9322166	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9377187	0.95[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9377188	0.81[CEU][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9399678	0.89[AMR][1000 genomes];0.85[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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10457074	SUMO4	cis	cerebellum	SCAN
rs10457074	C6orf97	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149339400-149364600	Weak transcription	Lung	lung
3	chr6:149341000-149365400	Weak transcription	Right Ventricle	heart
4	chr6:149345400-149362000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:149348000-149367400	Weak transcription	Primary B cells from cord blood	blood
6	chr6:149353800-149362400	Weak transcription	Pancreas	Pancrea
7	chr6:149353800-149367400	Weak transcription	Spleen	Spleen
8	chr6:149353800-149367800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:149353800-149369800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:149354000-149362000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:149354400-149400600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:149354600-149360600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:149354600-149372000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:149354800-149365200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:149354800-149366400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:149355000-149362400	Weak transcription	Aorta	Aorta
17	chr6:149355200-149360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:149355600-149361800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:149355800-149381600	Weak transcription	Right Atrium	heart
20	chr6:149357200-149362200	Weak transcription	HepG2	liver
21	chr6:149358200-149365400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:149358600-149367000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:149358600-149369000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:149358800-149361200	Weak transcription	Fetal Brain Male	brain
25	chr6:149358800-149367200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:149358800-149367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:149358800-149368000	Weak transcription	NHLF	lung
28	chr6:149359000-149360200	Weak transcription	NH-A	brain
29	chr6:149359000-149362200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:149359000-149362400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:149359000-149367200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:149359200-149360800	Weak transcription	Fetal Thymus	thymus
33	chr6:149359200-149362400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:149359200-149362400	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:149359200-149362600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:149359200-149364600	Weak transcription	HSMMtube	muscle
37	chr6:149359200-149365600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr6:149359200-149365600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:149359200-149367200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:149359200-149367600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:149359200-149372000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:149359200-149380200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:149359200-149380200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr6:149359200-149381400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:149359200-149381400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:149359200-149381600	Weak transcription	Ovary	ovary
47	chr6:149359200-149383600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:149359400-149360600	Weak transcription	Fetal Stomach	stomach
49	chr6:149359400-149363200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:149359400-149365200	Weak transcription	Colon Smooth Muscle	Colon

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