Variant report

Variant	rs9555696
Chromosome Location	chr13:111050335-111050336
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111042974..111045248-chr13:111048592..111050627,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1536622	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs28592869	0.86[AFR][1000 genomes]
rs4132949	0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4555010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773180	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61963204	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9559785	0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9559786	0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9559789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9559790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9559791	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9559792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9559793	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9559794	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2751128	chr13:111040798-111132490	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111040800-111050800	Weak transcription	Psoas Muscle	Psoas
2	chr13:111040800-111058000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:111041400-111058000	Weak transcription	Fetal Intestine Large	intestine
4	chr13:111043000-111057000	Weak transcription	NHEK	skin
5	chr13:111043000-111059200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:111043000-111060000	Weak transcription	A549	lung
7	chr13:111044000-111051000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:111045200-111056800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:111045600-111054200	Weak transcription	Spleen	Spleen
10	chr13:111045600-111054600	Weak transcription	HUVEC	blood vessel
11	chr13:111045600-111058200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:111045600-111059400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr13:111046800-111051600	Enhancers	Left Ventricle	heart
14	chr13:111047800-111050600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr13:111048200-111052200	Enhancers	Fetal Muscle Leg	muscle
16	chr13:111048400-111052400	Enhancers	Fetal Heart	heart
17	chr13:111048800-111050600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:111049000-111059600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr13:111049200-111051000	Enhancers	Fetal Muscle Trunk	muscle
20	chr13:111049200-111054800	Weak transcription	Fetal Intestine Small	intestine
21	chr13:111049400-111050400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:111049400-111050400	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr13:111049400-111050800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr13:111049600-111050400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr13:111049600-111050400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:111049600-111050400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr13:111049600-111050400	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr13:111049600-111050400	Flanking Active TSS	Colon Smooth Muscle	Colon
29	chr13:111049600-111050400	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr13:111049600-111050400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr13:111049600-111050400	Flanking Active TSS	HSMMtube	muscle
32	chr13:111049600-111050600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr13:111049600-111050600	Flanking Active TSS	NHLF	lung
34	chr13:111049600-111050800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr13:111049600-111051000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr13:111049600-111054800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:111049800-111050400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:111049800-111050400	Active TSS	Brain Anterior Caudate	brain
39	chr13:111049800-111051400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr13:111050000-111050400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr13:111050000-111050400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:111050000-111050400	Enhancers	Fetal Kidney	kidney
43	chr13:111050000-111050400	Active TSS	HSMM	muscle
44	chr13:111050000-111051600	Enhancers	NH-A	brain
45	chr13:111050000-111052200	Enhancers	Placenta	Placenta
46	chr13:111050200-111050400	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr13:111050200-111050400	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr13:111050200-111050400	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr13:111050200-111050400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
50	chr13:111050200-111050600	Active TSS	Fetal Lung	lung

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