Variant report

Variant	rs41524944
Chromosome Location	chr1:45122025-45122026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45119430..45122212-chr1:45185385..45187031,2	MCF-7	breast:
2	chr1:45114297..45117941-chr1:45118862..45123452,6	K562	blood:
3	chr1:45095204..45100641-chr1:45116393..45122089,10	MCF-7	breast:
4	chr1:45086965..45088510-chr1:45121277..45123002,2	MCF-7	breast:
5	chr1:45121876..45123394-chr1:45138815..45140382,2	MCF-7	breast:
6	chr1:45121448..45125334-chr1:45184794..45188657,5	K562	blood:

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

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12036630	1.00[EUR][1000 genomes]
rs1321703	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16832186	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16832188	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2281759	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs3444	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs3738733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3754421	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3768438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768439	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs3768441	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3850854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3889695	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41468751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4660284	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs4660285	0.94[ASN][1000 genomes]
rs4660286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660814	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4660819	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4660820	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs56756630	0.90[EUR][1000 genomes]
rs59834392	0.90[EUR][1000 genomes]
rs66509359	1.00[EUR][1000 genomes]
rs72671943	0.90[EUR][1000 genomes]
rs72671944	0.90[EUR][1000 genomes]
rs72671945	0.90[EUR][1000 genomes]
rs72671948	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72671949	0.87[AMR][1000 genomes]
rs72671950	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72671962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72671966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72671967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72671971	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72671974	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671982	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671984	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671988	1.00[EUR][1000 genomes]
rs7532001	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7539607	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45099800-45125600	Strong transcription	Lung	lung
2	chr1:45104000-45138200	Weak transcription	Fetal Brain Male	brain
3	chr1:45106800-45124800	Weak transcription	Fetal Heart	heart
4	chr1:45111200-45128000	Weak transcription	Right Atrium	heart
5	chr1:45113000-45126200	Weak transcription	Small Intestine	intestine
6	chr1:45113200-45125800	Strong transcription	Fetal Stomach	stomach
7	chr1:45114600-45130000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:45115000-45126000	Weak transcription	HMEC	breast
9	chr1:45115200-45137800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:45115600-45125800	Weak transcription	HSMM	muscle
11	chr1:45115800-45125000	Weak transcription	Fetal Kidney	kidney
12	chr1:45115800-45138000	Weak transcription	NHDF-Ad	bronchial
13	chr1:45116000-45124400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:45116000-45130000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:45116600-45127600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:45116800-45125800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:45117000-45125600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:45117200-45125000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:45117200-45125800	Weak transcription	Fetal Lung	lung
20	chr1:45117200-45127600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:45117200-45130200	Weak transcription	Primary B cells from cord blood	blood
22	chr1:45117200-45137800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:45117200-45138600	Weak transcription	Aorta	Aorta
24	chr1:45117400-45125800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:45117400-45125800	Weak transcription	HSMMtube	muscle
26	chr1:45117400-45129200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:45117400-45130200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:45117400-45130200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:45117400-45130200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:45117400-45138000	Weak transcription	Left Ventricle	heart
31	chr1:45117600-45130200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:45117800-45125200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:45117800-45125600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:45117800-45126000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:45117800-45128000	Weak transcription	Colonic Mucosa	Colon
36	chr1:45118000-45124600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:45118200-45130200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:45118400-45127600	Weak transcription	Thymus	Thymus
39	chr1:45118400-45129400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:45118400-45130000	Weak transcription	GM12878-XiMat	blood
41	chr1:45118400-45130200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:45118600-45124400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:45118600-45125800	Strong transcription	Fetal Intestine Small	intestine
44	chr1:45118600-45126000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:45118600-45138600	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:45118800-45122600	Weak transcription	Fetal Thymus	thymus
47	chr1:45119000-45122200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:45119000-45124200	Strong transcription	Liver	Liver
49	chr1:45119000-45128800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:45119200-45126800	Weak transcription	Primary hematopoietic stem cells	blood

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