Variant report

Variant	rs12507785
Chromosome Location	chr4:151418747-151418748
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	chr4:151411570..151413992-chr4:151416571..151418811,2	MCF-7	breast:
2	chr4:151416896..151419683-chr4:151431841..151434385,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12498862	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12499470	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12500337	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12502486	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12503093	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12506612	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508149	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12647325	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17504359	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17504442	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17589028	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17589134	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17589349	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1979920	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2036552	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2360071	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41386148	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56714695	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6535735	0.85[ASN][1000 genomes]
rs6812262	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6817796	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6827645	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6831707	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833359	0.85[ASN][1000 genomes]
rs6836012	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6839345	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849869	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6854612	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7677055	0.89[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs7681051	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7699001	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8180280	0.90[CHB][hapmap]
rs952097	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs998069	0.91[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	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv830112	chr4:151243801-151431771	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv869051	chr4:151347901-151737781	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1024820	chr4:151364078-151943561	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12507785	TTC29	cis	cerebellum	SCAN
rs12507785	FAM160A1	cis	parietal	SCAN
rs12507785	PLRG1	cis	parietal	SCAN
rs12507785	LRBA	cis	parietal	SCAN
rs12507785	LRBA	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151374400-151419000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:151382400-151422400	Weak transcription	Adipose Nuclei	Adipose
3	chr4:151385400-151442200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr4:151387600-151419000	Weak transcription	K562	blood
5	chr4:151387800-151423000	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:151392200-151424400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:151395400-151424000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:151400000-151434200	Weak transcription	Primary T cells from cord blood	blood
9	chr4:151400400-151422000	Weak transcription	Osteobl	bone
10	chr4:151408400-151422200	Weak transcription	Primary B cells from cord blood	blood
11	chr4:151409000-151422000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:151409000-151456600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:151410000-151444400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:151412000-151424200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:151412200-151424200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:151417000-151418800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:151418400-151419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:151418600-151419000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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