Variant report

Variant	rs7870049
Chromosome Location	chr9:94645758-94645759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94536230..94537049-chr9:94645022..94645936,2	MCF-7	breast:
2	chr9:94636703..94639887-chr9:94643001..94646217,3	K562	blood:
3	chr9:94633023..94637402-chr9:94642921..94647325,4	MCF-7	breast:
4	chr9:94631930..94633777-chr9:94645726..94647722,2	K562	blood:
5	chr9:94643211..94646019-chr9:94657149..94659875,2	K562	blood:
6	chr9:94645315..94647676-chr9:94666839..94670309,3	K562	blood:
7	chr9:94640107..94642644-chr9:94644861..94647641,2	K562	blood:

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

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

rs_ID	r²[population]
rs10116962	0.81[ASN][1000 genomes]
rs10761132	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10761133	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10761134	0.87[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs10761135	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10820906	0.81[CEU][hapmap]
rs10820910	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992124	0.80[CEU][hapmap]
rs10992131	0.80[CEU][hapmap]
rs10992132	0.80[CEU][hapmap]
rs10992134	0.97[GIH][hapmap];0.81[JPT][hapmap]
rs10992135	0.84[CEU][hapmap]
rs10992136	0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992137	0.80[CEU][hapmap]
rs10992139	0.80[CEU][hapmap]
rs10992144	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs10992145	0.83[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12551140	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs12555334	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12683797	0.80[CEU][hapmap]
rs12684524	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12684533	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1528363	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1528364	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534530	0.81[EUR][1000 genomes]
rs1534533	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1881385	0.90[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs1881392	0.80[CEU][hapmap]
rs2030991	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2312732	0.84[CEU][hapmap]
rs2312734	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs2312735	0.90[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4744107	0.81[JPT][hapmap]
rs4744109	0.88[CEU][hapmap]
rs4744110	0.84[CEU][hapmap]
rs4744111	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744112	0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4744113	0.80[CEU][hapmap]
rs55956910	0.81[EUR][1000 genomes]
rs58202197	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62565675	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479374	0.82[TSI][hapmap]
rs6479377	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479379	0.80[EUR][1000 genomes]
rs7029950	0.82[TSI][hapmap]
rs7030661	0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7031562	0.84[CEU][hapmap]
rs7045226	0.95[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7048756	0.83[CEU][hapmap]
rs7850118	0.84[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7856144	0.82[TSI][hapmap]
rs7858435	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7864311	0.81[EUR][1000 genomes]
rs7865855	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7867567	0.81[EUR][1000 genomes]
rs7874148	0.82[TSI][hapmap]

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	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7870049	ZNF484	cis	parietal	SCAN
rs7870049	SPTLC1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94627000-94650800	Weak transcription	Gastric	stomach
2	chr9:94627200-94648600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:94627600-94647400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:94636600-94646000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:94636600-94647200	Weak transcription	Fetal Intestine Large	intestine
6	chr9:94638200-94646200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:94638400-94646000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:94639800-94647400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:94642800-94646400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:94643200-94646000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:94643200-94650400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:94643400-94648600	Weak transcription	Pancreas	Pancrea
13	chr9:94643600-94646400	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:94644200-94646000	Weak transcription	Fetal Lung	lung
15	chr9:94644400-94645800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:94644400-94646000	Weak transcription	Ovary	ovary
17	chr9:94644400-94650800	Weak transcription	Right Atrium	heart
18	chr9:94644800-94647600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:94645200-94646600	Weak transcription	Fetal Stomach	stomach
20	chr9:94645200-94647200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:94645400-94646400	Weak transcription	Fetal Intestine Small	intestine
22	chr9:94645400-94646600	Enhancers	Fetal Heart	heart
23	chr9:94645400-94648600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:94645400-94648800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:94645600-94646000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:94645600-94646000	Weak transcription	K562	blood

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