Variant report

Variant	rs12568405
Chromosome Location	chr1:94095338-94095339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94094810..94095721-chr1:94145946..94146885,3	MCF-7	breast:
2	chr1:94092851..94096597-chr1:94146302..94147993,4	MCF-7	breast:
3	chr1:94094795..94095616-chr1:94309558..94310553,5	K562	blood:
4	chr1:93903343..93903897-chr1:94095076..94095604,2	K562	blood:
5	chr1:94094804..94095480-chr1:94309483..94310060,2	MCF-7	breast:
6	chr1:94093742..94096108-chr1:94309968..94312070,2	K562	blood:
7	chr1:94095273..94097251-chr1:94284521..94286111,2	MCF-7	breast:
8	chr1:94091548..94098915-chr1:94308687..94313875,7	K562	blood:
9	chr1:94094533..94095758-chr1:94278266..94279023,3	MCF-7	breast:
10	chr1:94094814..94095807-chr1:94279301..94280178,3	MCF-7	breast:
11	chr1:94092980..94095729-chr1:94311272..94313318,3	MCF-7	breast:
12	chr1:94094709..94095433-chr1:94279409..94280490,4	MCF-7	breast:
13	chr1:94093897..94096295-chr1:94277751..94279857,3	MCF-7	breast:
14	chr1:94095088..94095631-chr1:94310611..94311193,2	MCF-7	breast:
15	chr1:94094703..94095710-chr1:94279237..94280002,9	K562	blood:

No data

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

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12084853	1.00[JPT][hapmap]
rs1618866	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17110076	0.81[EUR][1000 genomes]
rs1740068	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1772781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1772782	0.93[ASN][1000 genomes]
rs182913	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs183538	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295330	0.81[EUR][1000 genomes]
rs236266	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs236267	0.89[ASN][1000 genomes]
rs236270	0.87[ASN][1000 genomes]
rs236271	0.87[ASN][1000 genomes]
rs236274	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236275	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236277	0.89[ASN][1000 genomes]
rs236278	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236281	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236284	1.00[JPT][hapmap]
rs236287	1.00[JPT][hapmap]
rs236295	1.00[JPT][hapmap]
rs236296	1.00[JPT][hapmap]
rs236307	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs236308	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs236312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs236313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs236343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs236344	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs368888	0.83[ASN][1000 genomes]
rs3754189	0.81[EUR][1000 genomes]
rs3767973	0.94[EUR][1000 genomes]
rs3767979	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767991	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3767993	0.83[AMR][1000 genomes]
rs399649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs423493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6541387	1.00[JPT][hapmap]
rs6657709	1.00[JPT][hapmap]
rs6660740	1.00[JPT][hapmap]
rs6674143	0.81[EUR][1000 genomes]
rs6702036	1.00[JPT][hapmap]
rs6704479	1.00[JPT][hapmap]
rs7524368	0.94[EUR][1000 genomes]
rs798213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

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:66 , 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	chr1:94077200-94099000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:94083400-94108200	Weak transcription	Esophagus	oesophagus
4	chr1:94083600-94101600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:94084200-94101000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:94085400-94107600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:94086800-94098000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:94086800-94101200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:94088200-94095600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:94088400-94096400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:94088400-94100400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:94088600-94118800	Weak transcription	Gastric	stomach
13	chr1:94089600-94097400	Genic enhancers	NHEK	skin
14	chr1:94090400-94101400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:94090600-94101400	Weak transcription	Right Ventricle	heart
16	chr1:94091200-94095600	Enhancers	HUVEC	blood vessel
17	chr1:94091400-94097000	Weak transcription	HepG2	liver
18	chr1:94091600-94101000	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:94091600-94101400	Weak transcription	Brain Angular Gyrus	brain
20	chr1:94091600-94106600	Weak transcription	Aorta	Aorta
21	chr1:94091600-94107600	Weak transcription	Ovary	ovary
22	chr1:94091800-94117400	Weak transcription	Fetal Lung	lung
23	chr1:94092200-94097000	Weak transcription	Placenta	Placenta
24	chr1:94092200-94097800	Genic enhancers	HMEC	breast
25	chr1:94092200-94100400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:94092200-94101000	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:94092400-94097000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:94093000-94095400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:94093000-94100400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:94093200-94096400	Weak transcription	Fetal Intestine Small	intestine
31	chr1:94093200-94100600	Weak transcription	Brain Substantia Nigra	brain
32	chr1:94093600-94096000	Enhancers	Osteobl	bone
33	chr1:94093600-94096400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:94093600-94097800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:94093800-94095400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:94093800-94095600	Enhancers	NH-A	brain
37	chr1:94093800-94097800	Genic enhancers	Muscle Satellite Cultured Cells	--
38	chr1:94093800-94098000	Genic enhancers	Hela-S3	cervix
39	chr1:94094000-94100400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:94094000-94100400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:94094000-94101200	Weak transcription	Left Ventricle	heart
42	chr1:94094200-94096600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:94094200-94101200	Weak transcription	Lung	lung
44	chr1:94094200-94101200	Weak transcription	Right Atrium	heart
45	chr1:94094200-94120400	Weak transcription	Psoas Muscle	Psoas
46	chr1:94094400-94095400	Enhancers	Adipose Nuclei	Adipose
47	chr1:94094400-94095600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:94094400-94095600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:94094400-94096600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:94094600-94095600	Enhancers	NHLF	lung

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