Variant report

Variant	rs9367440
Chromosome Location	chr6:13365913-13365914
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13364126..13366714-chr6:13711205..13713742,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10807431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10807432	0.87[EUR][1000 genomes]
rs10948650	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12153966	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2439536	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2496139	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2496160	0.91[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2496161	0.91[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2496162	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2496173	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28813108	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711978	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs474159	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs476904	0.91[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs489396	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs491278	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs492433	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs501987	0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[EUR][1000 genomes]
rs510932	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs516003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517803	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs524118	0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs531256	0.91[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs548119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552655	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs553671	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs553948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs560396	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs564174	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs570315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579028	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760579	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7770078	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs821276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357708	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13355600-13383400	Weak transcription	A549	lung
2	chr6:13356200-13367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:13356200-13371800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:13356200-13372000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:13356200-13373600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:13356200-13378200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:13356400-13368000	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:13358000-13371800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:13358200-13367600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:13358200-13368200	Weak transcription	HMEC	breast
11	chr6:13358400-13367600	Weak transcription	NH-A	brain
12	chr6:13358800-13367400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:13359000-13367600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:13359200-13367400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:13359200-13367600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:13359200-13367600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:13359200-13367600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:13359400-13367400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:13359400-13367600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:13360800-13370800	Weak transcription	HepG2	liver
21	chr6:13361400-13367400	Weak transcription	HUVEC	blood vessel
22	chr6:13361600-13378200	Weak transcription	Fetal Thymus	thymus
23	chr6:13361800-13367600	Weak transcription	Psoas Muscle	Psoas
24	chr6:13362400-13368600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr6:13362800-13366000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:13362800-13366000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:13362800-13366000	Strong transcription	Liver	Liver
28	chr6:13362800-13366600	Strong transcription	GM12878-XiMat	blood
29	chr6:13363200-13367600	Weak transcription	Placenta	Placenta
30	chr6:13363400-13368600	Weak transcription	HSMM	muscle
31	chr6:13363600-13368200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:13364200-13366000	Genic enhancers	Right Ventricle	heart
33	chr6:13364200-13366200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:13364400-13366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:13364400-13366000	Strong transcription	Fetal Stomach	stomach
36	chr6:13364400-13367400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:13364600-13366000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:13364600-13366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:13364600-13366000	Strong transcription	Aorta	Aorta
40	chr6:13364600-13366000	Strong transcription	NHLF	lung
41	chr6:13364800-13366000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:13364800-13366000	Strong transcription	Colonic Mucosa	Colon
43	chr6:13364800-13366000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:13364800-13367600	Weak transcription	Right Atrium	heart
45	chr6:13364800-13367600	Weak transcription	Stomach Mucosa	stomach
46	chr6:13365000-13366000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr6:13365000-13366000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:13365000-13366000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:13365000-13366000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:13365000-13366000	Strong transcription	Ovary	ovary

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