Variant report

Variant	rs1536580
Chromosome Location	chr6:20207926-20207927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr6:20207880-20208127	T-47D	breast:	n/a	n/a
2	FOXA1	chr6:20207880-20208107	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:20117949..20119536-chr6:20206647..20209362,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227803	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1077919	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1077920	1.00[ASN][1000 genomes]
rs1536581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928120	0.92[ASN][1000 genomes]
rs9350222	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9350223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358312	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029729	chr6:20113226-20235122	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538155	chr6:20113226-20235122	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1033904	chr6:20127596-20210374	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1799840	chr6:20196549-20210374	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1027355	chr6:20207893-20261048	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1536580	PRL	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:20193000-20209200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:20199400-20210000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:20200600-20209200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr6:20201400-20210800	Weak transcription	Fetal Stomach	stomach
5	chr6:20201800-20209000	Weak transcription	Fetal Lung	lung
6	chr6:20202600-20211200	Enhancers	Stomach Mucosa	stomach
7	chr6:20203200-20210400	Weak transcription	Fetal Kidney	kidney
8	chr6:20203200-20211200	Weak transcription	Liver	Liver
9	chr6:20203200-20211200	Weak transcription	NHDF-Ad	bronchial
10	chr6:20203600-20208000	Enhancers	Rectal Smooth Muscle	rectum
11	chr6:20203600-20210400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:20203800-20208200	Enhancers	Ovary	ovary
13	chr6:20204000-20208200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr6:20204400-20210000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:20204400-20210400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:20204600-20208800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:20204600-20211000	Weak transcription	HMEC	breast
18	chr6:20204600-20211200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:20204600-20211200	Weak transcription	A549	lung
20	chr6:20204800-20210000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:20204800-20211200	Enhancers	Fetal Heart	heart
22	chr6:20205000-20211200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:20205200-20209600	Weak transcription	NHEK	skin
24	chr6:20205200-20210000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:20205400-20210000	Weak transcription	Left Ventricle	heart
26	chr6:20205600-20208200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:20205800-20208200	Enhancers	K562	blood
28	chr6:20206000-20208200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr6:20206200-20209600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:20206400-20209000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:20206400-20210000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:20206400-20210000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:20206400-20210000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:20206400-20210000	Weak transcription	Gastric	stomach
35	chr6:20206400-20211200	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:20206400-20211200	Weak transcription	Pancreas	Pancrea
37	chr6:20206600-20208000	Flanking Active TSS	GM12878-XiMat	blood
38	chr6:20206600-20211200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:20206800-20211200	Weak transcription	Placenta	Placenta
40	chr6:20206800-20211400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:20207000-20210000	Weak transcription	Adipose Nuclei	Adipose
42	chr6:20207000-20210000	Weak transcription	Colonic Mucosa	Colon
43	chr6:20207000-20210000	Weak transcription	Esophagus	oesophagus
44	chr6:20207200-20209400	Enhancers	Colon Smooth Muscle	Colon
45	chr6:20207200-20210000	Weak transcription	Lung	lung
46	chr6:20207200-20211200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:20207200-20211200	Weak transcription	Spleen	Spleen
48	chr6:20207400-20208200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr6:20207400-20211200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr6:20207600-20208000	Enhancers	Primary hematopoietic stem cells	blood

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