Variant report

Variant	rs9404003
Chromosome Location	chr6:149235313-149235314
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	chr6:149233576..149235247-chr6:149235248..149237823,2	MCF-7	breast:
2	chr6:149235031..149236841-chr6:149238343..149239900,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17721845	0.83[LWK][hapmap];0.90[YRI][hapmap]
rs4333438	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9377174	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9377175	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9377176	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9377177	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9390628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9390629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390630	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9390633	0.82[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9399670	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399674	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9403999	0.82[CHB][hapmap]
rs9404002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv464074	chr6:149211090-149242095	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv604844	chr6:149211090-149242095	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv464075	chr6:149221294-149242095	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv470865	chr6:149221294-149242095	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv604845	chr6:149221294-149242095	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9404003	UST	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149207800-149237400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:149209000-149247600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:149210200-149240200	Weak transcription	Primary B cells from cord blood	blood
4	chr6:149211600-149255400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:149217600-149236800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:149226600-149252800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:149226600-149255600	Weak transcription	Ovary	ovary
8	chr6:149227200-149236400	Weak transcription	Fetal Stomach	stomach
9	chr6:149227400-149240400	Weak transcription	Pancreas	Pancrea
10	chr6:149230800-149238000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:149230800-149244600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:149231000-149237000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:149231000-149244200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:149231000-149245400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:149231200-149236600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:149232600-149236000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:149234000-149236400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:149234200-149236800	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:149234200-149244600	Weak transcription	Fetal Heart	heart
20	chr6:149234200-149245800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:149234400-149245000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr6:149235000-149235400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:149235000-149235400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
24	chr6:149235000-149244000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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