Variant report

Variant	rs544430
Chromosome Location	chr1:225761403-225761404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225759930..225762084-chr1:225837914..225840805,3	MCF-7	breast:
2	chr1:225759882..225763061-chr1:225838527..225842232,4	MCF-7	breast:
3	chr1:225737824..225740391-chr1:225760266..225761953,2	K562	blood:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10082003	0.83[AMR][1000 genomes]
rs10915853	0.85[AMR][1000 genomes]
rs12071529	0.84[AFR][1000 genomes]
rs1222434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1222439	0.86[EUR][1000 genomes]
rs1336480	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360958	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764345	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1764347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1771318	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2035916	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3904084	1.00[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs475794	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs481746	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516323	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525062	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526221	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566085	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59363938	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7545317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9651009	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv511737	chr1:225759933-225763071	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
3	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:225734600-225763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:225744800-225768200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:225744800-225768600	Weak transcription	Fetal Brain Male	brain
7	chr1:225745000-225770000	Weak transcription	HUVEC	blood vessel
8	chr1:225745000-225772800	Weak transcription	Fetal Brain Female	brain
9	chr1:225747800-225765000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:225748800-225765800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:225754000-225764600	Weak transcription	Fetal Stomach	stomach
14	chr1:225754200-225764400	Weak transcription	Right Atrium	heart
15	chr1:225754200-225764600	Weak transcription	Ovary	ovary
16	chr1:225754400-225764400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:225754400-225769400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:225754600-225764400	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:225754600-225766000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:225755200-225763800	Weak transcription	Left Ventricle	heart
21	chr1:225755200-225766000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:225755200-225772200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:225755400-225765000	Weak transcription	HSMM	muscle
24	chr1:225756600-225765000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:225756600-225767600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:225756800-225764400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:225756800-225765400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:225757000-225764200	Weak transcription	NHDF-Ad	bronchial
29	chr1:225757000-225764400	Weak transcription	Fetal Heart	heart
30	chr1:225757000-225765000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:225757000-225765000	Weak transcription	NHLF	lung
32	chr1:225758200-225764600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:225758200-225765800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:225758600-225765000	Weak transcription	Brain Germinal Matrix	brain
35	chr1:225759400-225769600	Weak transcription	Lung	lung
36	chr1:225759600-225787600	Weak transcription	Fetal Intestine Small	intestine
37	chr1:225760000-225761600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:225760000-225762000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr1:225760000-225763600	Weak transcription	Psoas Muscle	Psoas
40	chr1:225760000-225764200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:225760000-225764400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:225760000-225764400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:225760000-225764400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:225760000-225765000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:225760000-225769800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:225760200-225761600	Enhancers	A549	lung
48	chr1:225760200-225761600	Enhancers	NH-A	brain
49	chr1:225760200-225761800	Enhancers	Brain Hippocampus Middle	brain
50	chr1:225760200-225762200	Enhancers	Osteobl	bone

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