Variant report

Variant	rs4318907
Chromosome Location	chr6:149355453-149355454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149352653..149356079-chr6:149835245..149838856,4	MCF-7	breast:
2	chr6:149353960..149356786-chr6:149766378..149768113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252244	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10457074	0.95[CEU][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10872629	0.80[AMR][1000 genomes]
rs1317171	0.86[CEU][hapmap];0.96[MEX][hapmap];0.84[AMR][1000 genomes]
rs1934224	0.91[CEU][hapmap]
rs2275423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2340751	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2340752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2340798	0.86[CEU][hapmap]
rs2340801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2340802	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2879843	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4377808	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897074	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897076	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6570920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6904550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6911303	0.83[JPT][hapmap]
rs6915298	0.86[CEU][hapmap];0.96[MEX][hapmap];0.80[AMR][1000 genomes]
rs6930989	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6931675	0.86[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap]
rs6931744	0.95[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6935330	0.96[MEX][hapmap]
rs6936176	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7738162	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs7747463	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7748978	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7761119	0.91[MEX][hapmap]
rs7765778	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7774457	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7774887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7776117	0.86[CEU][hapmap];0.84[AMR][1000 genomes]
rs9285516	0.82[CEU][hapmap];0.96[MEX][hapmap]
rs9377187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9377188	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[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	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
rs4318907	SUMO4	cis	cerebellum	SCAN
rs4318907	C6orf97	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149336200-149358000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:149337600-149358000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:149339400-149364600	Weak transcription	Lung	lung
5	chr6:149341000-149365400	Weak transcription	Right Ventricle	heart
6	chr6:149343200-149358000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:149344000-149357200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:149344000-149357400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:149344600-149357800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:149344800-149358000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:149345400-149362000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:149345600-149358000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:149347800-149356800	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:149348000-149367400	Weak transcription	Primary B cells from cord blood	blood
15	chr6:149350200-149357600	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:149350400-149358000	Weak transcription	Fetal Kidney	kidney
17	chr6:149352400-149355600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:149352800-149355600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr6:149352800-149355800	Enhancers	Fetal Lung	lung
20	chr6:149353000-149355800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:149353000-149355800	Enhancers	Ovary	ovary
22	chr6:149353400-149355800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:149353600-149357200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:149353800-149355800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:149353800-149356000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:149353800-149356000	Enhancers	Dnd41	blood
27	chr6:149353800-149356800	Weak transcription	Fetal Stomach	stomach
28	chr6:149353800-149357200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:149353800-149357400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:149353800-149358000	Enhancers	HSMMtube	muscle
31	chr6:149353800-149362400	Weak transcription	Pancreas	Pancrea
32	chr6:149353800-149367400	Weak transcription	Spleen	Spleen
33	chr6:149353800-149367800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:149353800-149369800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:149354000-149356600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:149354000-149357000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:149354000-149358200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:149354000-149358200	Weak transcription	Fetal Thymus	thymus
39	chr6:149354000-149358400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:149354000-149362000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:149354200-149357200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr6:149354400-149358200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:149354400-149400600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:149354600-149360600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:149354600-149372000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:149354800-149355800	Enhancers	Osteobl	bone
47	chr6:149354800-149356400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:149354800-149357200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:149354800-149357200	Enhancers	HepG2	liver
50	chr6:149354800-149358200	Enhancers	Muscle Satellite Cultured Cells	--

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