Variant report

Variant	rs6936420
Chromosome Location	chr6:13417746-13417747
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	chr6:13417373..13420298-chr6:13574517..13576423,2	MCF-7	breast:
2	chr6:13415611..13418241-chr6:13485753..13488399,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12527593	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12528480	1.00[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs16874132	0.82[CEU][hapmap]
rs16874136	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs16874138	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs16874139	0.82[CEU][hapmap]
rs16874145	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs16874152	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs16874153	0.82[CEU][hapmap]
rs16874155	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1992387	0.82[CEU][hapmap]
rs511996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6914294	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs6926083	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs73366922	0.92[EUR][1000 genomes]
rs7746830	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7750943	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370100	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:13408600-13422600	Weak transcription	HSMM	muscle
5	chr6:13408800-13419400	Weak transcription	Primary B cells from cord blood	blood
6	chr6:13408800-13420200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:13408800-13423000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:13411400-13419600	Weak transcription	Fetal Thymus	thymus
9	chr6:13411400-13421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:13411600-13424200	Enhancers	Right Ventricle	heart
11	chr6:13412200-13419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:13413200-13417800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:13413600-13419400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:13413600-13419800	Weak transcription	Esophagus	oesophagus
15	chr6:13413800-13417800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:13413800-13419600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:13414000-13420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:13414000-13421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:13414000-13421800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:13414000-13421800	Weak transcription	Brain Germinal Matrix	brain
21	chr6:13414000-13422000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:13414200-13417800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:13414600-13422000	Weak transcription	NHLF	lung
24	chr6:13414800-13419200	Weak transcription	Fetal Brain Female	brain
25	chr6:13414800-13420200	Weak transcription	HSMMtube	muscle
26	chr6:13415000-13417800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:13415000-13418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:13415000-13419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:13415000-13419200	Weak transcription	NHEK	skin
30	chr6:13415000-13420000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:13415000-13420400	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:13415200-13417800	Weak transcription	Adipose Nuclei	Adipose
33	chr6:13415200-13418800	Weak transcription	Fetal Brain Male	brain
34	chr6:13415200-13419400	Enhancers	Stomach Smooth Muscle	stomach
35	chr6:13415200-13419600	Weak transcription	Primary T cells from cord blood	blood
36	chr6:13415200-13420200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:13415400-13419000	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:13415400-13419200	Weak transcription	Fetal Stomach	stomach
39	chr6:13415400-13419400	Weak transcription	Fetal Lung	lung
40	chr6:13415400-13422600	Weak transcription	Gastric	stomach
41	chr6:13415600-13417800	Weak transcription	Pancreas	Pancrea
42	chr6:13415600-13419000	Weak transcription	Aorta	Aorta
43	chr6:13415800-13417800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:13415800-13417800	Weak transcription	Lung	lung
45	chr6:13415800-13417800	Weak transcription	Psoas Muscle	Psoas
46	chr6:13415800-13417800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:13415800-13418800	Weak transcription	Fetal Heart	heart
48	chr6:13415800-13418800	Weak transcription	Spleen	Spleen
49	chr6:13415800-13419200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:13416000-13417800	Weak transcription	Brain Inferior Temporal Lobe	brain

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