Variant report

Variant	rs3778404
Chromosome Location	chr6:166970767-166970768
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	chr6:166969437..166971704-chr6:167039008..167042376,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071242	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1543802	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs2032546	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3778402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3799612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3799613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3799620	0.83[CHB][hapmap]
rs3799630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9348148	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9459695	0.88[CHB][hapmap];0.82[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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv5592	chr6:166958317-167002951	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166960000-166972800	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:166964800-166972000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:166965600-166971000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:166965800-166972400	Enhancers	Fetal Muscle Leg	muscle
5	chr6:166966000-166973600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:166966000-166974200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:166966200-166971200	Enhancers	Left Ventricle	heart
8	chr6:166966200-166978000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:166966400-166970800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:166966600-166970800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:166967000-166971200	Enhancers	Brain Angular Gyrus	brain
12	chr6:166967600-166971000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:166967600-166971000	Enhancers	Adipose Nuclei	Adipose
14	chr6:166967600-166971000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:166967600-166971800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:166968000-166972000	Enhancers	Spleen	Spleen
17	chr6:166968000-166972800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:166968200-166972400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:166968400-166985800	Weak transcription	Fetal Kidney	kidney
20	chr6:166968800-166970800	Enhancers	HSMMtube	muscle
21	chr6:166968800-166971000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:166968800-166971600	Weak transcription	NHLF	lung
23	chr6:166968800-166973800	Enhancers	HMEC	breast
24	chr6:166969000-166970800	Enhancers	Gastric	stomach
25	chr6:166969000-166971000	Enhancers	Psoas Muscle	Psoas
26	chr6:166969000-166971000	Enhancers	Right Atrium	heart
27	chr6:166969000-166972400	Enhancers	Fetal Muscle Trunk	muscle
28	chr6:166969000-166973800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:166969000-166974000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:166969200-166972200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:166969200-166972200	Enhancers	Esophagus	oesophagus
32	chr6:166969400-166978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:166969600-166971800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:166969800-166971600	Weak transcription	Fetal Stomach	stomach
35	chr6:166969800-166971800	Enhancers	NH-A	brain
36	chr6:166970000-166971000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:166970000-166971000	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr6:166970000-166971000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr6:166970000-166971000	Enhancers	Hela-S3	cervix
40	chr6:166970000-166971000	Flanking Active TSS	Osteobl	bone
41	chr6:166970000-166971200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:166970200-166970800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:166970200-166970800	Bivalent Enhancer	Placenta	Placenta
44	chr6:166970200-166971000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:166970200-166971000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:166970200-166976200	Weak transcription	Right Ventricle	heart
47	chr6:166970400-166970800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:166970400-166970800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr6:166970400-166970800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:166970400-166970800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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