Variant report

Variant	rs3444
Chromosome Location	chr1:45119965-45119966
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45096840..45099376-chr1:45118064..45121315,3	MCF-7	breast:
2	chr1:45119430..45122212-chr1:45185385..45187031,2	MCF-7	breast:
3	chr1:45118835..45121657-chr1:45126816..45128426,2	MCF-7	breast:
4	chr1:45114297..45117941-chr1:45118862..45123452,6	K562	blood:
5	chr1:45095204..45100641-chr1:45116393..45122089,10	MCF-7	breast:
6	chr1:45115442..45121440-chr1:45183545..45188680,13	K562	blood:
7	chr1:45118903..45121400-chr1:45139420..45141294,2	K562	blood:
8	chr1:45118954..45120694-chr1:45122817..45124931,3	K562	blood:
9	chr1:45074258..45077660-chr1:45118753..45120788,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198520	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000187147	Chromatin interaction
ENSG00000126106	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1051648	0.95[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs11581172	0.95[CEU][hapmap];0.90[GIH][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs11582970	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11588956	0.82[TSI][hapmap]
rs12731688	0.90[EUR][1000 genomes]
rs1321703	0.89[CHD][hapmap]
rs1407144	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16832186	1.00[CHD][hapmap]
rs16832188	0.89[CHD][hapmap]
rs17387413	0.95[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs2018706	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs2236219	0.82[TSI][hapmap]
rs2281759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2355365	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2822	0.95[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs34296911	0.92[EUR][1000 genomes]
rs35791258	0.92[EUR][1000 genomes]
rs3738733	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3768438	0.87[ASN][1000 genomes]
rs3768439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3850852	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs3850854	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3889695	0.89[CHD][hapmap]
rs41269061	0.93[EUR][1000 genomes]
rs41468751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs41524944	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs4660283	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs4660284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660285	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4660286	0.88[ASN][1000 genomes]
rs4660815	0.90[CEU][hapmap];0.87[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs4660816	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs4660817	0.93[EUR][1000 genomes]
rs57291201	0.90[EUR][1000 genomes]
rs72671954	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72671962	0.94[ASN][1000 genomes]
rs72671966	0.91[ASN][1000 genomes]
rs72671967	0.90[ASN][1000 genomes]
rs72671971	0.88[ASN][1000 genomes]
rs74070566	0.83[EUR][1000 genomes]
rs7532001	0.86[JPT][hapmap]
rs876511	0.92[EUR][1000 genomes]
rs876512	0.92[EUR][1000 genomes]
rs995089	0.95[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45099400-45120800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:45099400-45121000	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:45099400-45121200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:45099800-45121200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:45099800-45121600	Strong transcription	Brain Germinal Matrix	brain
6	chr1:45099800-45125600	Strong transcription	Lung	lung
7	chr1:45100400-45120800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:45103600-45121400	Strong transcription	Fetal Brain Female	brain
9	chr1:45104000-45138200	Weak transcription	Fetal Brain Male	brain
10	chr1:45106800-45124800	Weak transcription	Fetal Heart	heart
11	chr1:45107800-45121000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:45108800-45121000	Strong transcription	Gastric	stomach
13	chr1:45109600-45121600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:45110200-45120000	Weak transcription	NH-A	brain
15	chr1:45111200-45120800	Strong transcription	Adipose Nuclei	Adipose
16	chr1:45111200-45128000	Weak transcription	Right Atrium	heart
17	chr1:45112000-45121400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:45113000-45126200	Weak transcription	Small Intestine	intestine
19	chr1:45113200-45125800	Strong transcription	Fetal Stomach	stomach
20	chr1:45113800-45121200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:45114600-45130000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:45114800-45120800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:45115000-45126000	Weak transcription	HMEC	breast
24	chr1:45115200-45137800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:45115600-45125800	Weak transcription	HSMM	muscle
26	chr1:45115800-45125000	Weak transcription	Fetal Kidney	kidney
27	chr1:45115800-45138000	Weak transcription	NHDF-Ad	bronchial
28	chr1:45116000-45124400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:45116000-45130000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:45116200-45120800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:45116200-45121400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:45116600-45120800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:45116600-45127600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:45116800-45120000	Weak transcription	Pancreas	Pancrea
35	chr1:45116800-45121200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:45116800-45121800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:45116800-45122000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:45116800-45125800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:45117000-45120000	Weak transcription	Esophagus	oesophagus
40	chr1:45117000-45125600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:45117200-45120000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:45117200-45125000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:45117200-45125800	Weak transcription	Fetal Lung	lung
44	chr1:45117200-45127600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:45117200-45130200	Weak transcription	Primary B cells from cord blood	blood
46	chr1:45117200-45137800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:45117200-45138600	Weak transcription	Aorta	Aorta
48	chr1:45117400-45120200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:45117400-45120600	Weak transcription	HepG2	liver
50	chr1:45117400-45125800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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