Variant report

Variant	rs3767979
Chromosome Location	chr1:94076919-94076920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94073816..94077242-chr1:94077483..94081240,4	MCF-7	breast:
2	chr1:94075553..94077277-chr1:94206889..94209236,2	MCF-7	breast:
3	chr1:94076543..94079128-chr1:94244196..94245876,2	MCF-7	breast:
4	chr1:94074918..94076929-chr1:94311455..94313305,2	MCF-7	breast:
5	chr1:94076613..94078527-chr1:94088033..94090133,2	MCF-7	breast:
6	chr1:94075678..94077839-chr1:94077927..94082069,3	K562	blood:
7	chr1:94074700..94077458-chr1:94080437..94082607,3	K562	blood:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12084853	0.89[JPT][hapmap]
rs12568405	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1618866	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17110076	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1740068	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1772781	0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1772782	0.82[ASN][1000 genomes]
rs182913	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs183538	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2295330	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs236266	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs236274	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs236275	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs236278	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs236281	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs236284	0.88[JPT][hapmap]
rs236287	0.88[JPT][hapmap]
rs236295	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs236296	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs236306	0.86[CHB][hapmap]
rs236307	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs236308	0.88[CHB][hapmap]
rs236312	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs236313	0.88[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs236343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs236344	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs3754189	0.81[EUR][1000 genomes]
rs3767973	0.94[EUR][1000 genomes]
rs3767981	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767987	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767991	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs399649	0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs423493	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs57012808	0.94[EUR][1000 genomes]
rs57466479	0.94[EUR][1000 genomes]
rs57914444	0.94[EUR][1000 genomes]
rs59777284	0.94[EUR][1000 genomes]
rs60159857	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6541380	1.00[CEU][hapmap]
rs6541387	0.89[JPT][hapmap]
rs6657709	0.88[JPT][hapmap]
rs6660740	0.88[JPT][hapmap]
rs6674143	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6699020	1.00[CEU][hapmap]
rs6702036	0.89[JPT][hapmap]
rs6704479	0.86[JPT][hapmap]
rs7524368	0.94[EUR][1000 genomes]
rs798213	0.88[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:94060200-94078800	Weak transcription	Colonic Mucosa	Colon
3	chr1:94061200-94078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:94066400-94079200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:94066400-94079600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:94068200-94079200	Genic enhancers	HSMM	muscle
7	chr1:94070800-94079200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:94071600-94079400	Weak transcription	Small Intestine	intestine
9	chr1:94071800-94078200	Enhancers	Liver	Liver
10	chr1:94071800-94079200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:94071800-94079800	Weak transcription	Fetal Kidney	kidney
12	chr1:94072200-94078400	Enhancers	Adipose Nuclei	Adipose
13	chr1:94072200-94079000	Enhancers	NHDF-Ad	bronchial
14	chr1:94072200-94079400	Weak transcription	Fetal Intestine Large	intestine
15	chr1:94072600-94078800	Enhancers	Fetal Muscle Leg	muscle
16	chr1:94072800-94078400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:94073000-94077600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:94073200-94077000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr1:94073600-94079200	Genic enhancers	HMEC	breast
20	chr1:94074200-94077600	Weak transcription	Fetal Brain Male	brain
21	chr1:94074200-94077600	Weak transcription	Stomach Mucosa	stomach
22	chr1:94074400-94077200	Weak transcription	Brain Germinal Matrix	brain
23	chr1:94074600-94078800	Weak transcription	Fetal Lung	lung
24	chr1:94074600-94079400	Weak transcription	Pancreas	Pancrea
25	chr1:94074800-94078600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:94074800-94079200	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:94075000-94079200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:94075000-94079200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:94075200-94079400	Weak transcription	Esophagus	oesophagus
30	chr1:94075400-94077800	Weak transcription	NH-A	brain
31	chr1:94075400-94078200	Weak transcription	NHLF	lung
32	chr1:94075400-94078800	Weak transcription	Ovary	ovary
33	chr1:94075400-94079200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:94075400-94079800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:94075400-94080000	Weak transcription	Fetal Thymus	thymus
36	chr1:94075600-94077600	Weak transcription	Right Ventricle	heart
37	chr1:94075600-94077600	Weak transcription	Spleen	Spleen
38	chr1:94075600-94077800	Weak transcription	Fetal Stomach	stomach
39	chr1:94075600-94078000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:94075600-94078200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:94075600-94078800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:94075600-94079200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:94075600-94079600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:94075600-94079800	Weak transcription	Lung	lung
45	chr1:94075600-94080600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:94075800-94077000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:94075800-94077000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:94075800-94077200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:94075800-94077400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:94075800-94077400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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