Variant report

Variant	rs1040563
Chromosome Location	chr1:210472956-210472957
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:210472845-210473249	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF7L2	chr1:210472946-210473300	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr1:210472844-210473400	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:210467411..210469958-chr1:210471110..210473541,2	K562	blood:
2	chr1:210472726..210476795-chr1:210544838..210548404,4	MCF-7	breast:
3	chr1:210472681..210476140-chr1:210544335..210548471,5	K562	blood:
4	chr1:210468377..210470093-chr1:210472227..210474687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233455	TF binding region
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12739013	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12739023	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1338285	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs655829	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs655847	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs656753	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6658075	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs670441	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210466600-210474200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:210466800-210477400	Enhancers	Fetal Muscle Leg	muscle
3	chr1:210468200-210475000	Weak transcription	Ovary	ovary
4	chr1:210468600-210473600	Weak transcription	Lung	lung
5	chr1:210468600-210474200	Weak transcription	Brain Substantia Nigra	brain
6	chr1:210468800-210473400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:210468800-210474200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:210468800-210474200	Weak transcription	Stomach Mucosa	stomach
9	chr1:210469000-210474200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:210469000-210474400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:210469200-210473000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:210469400-210473000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:210469400-210475200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:210469600-210475000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:210470000-210474000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:210470400-210473400	Weak transcription	Esophagus	oesophagus
17	chr1:210471600-210473000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:210471800-210474400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:210472000-210473400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr1:210472200-210475000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:210472200-210475200	Enhancers	NHEK	skin
22	chr1:210472400-210473400	Enhancers	HMEC	breast
23	chr1:210472400-210474000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:210472400-210475400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:210472400-210477000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:210472600-210473200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:210472600-210473400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:210472600-210473400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:210472600-210473600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:210472600-210474200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:210472600-210475200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr1:210472800-210473000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:210472800-210473200	Bivalent Enhancer	Brain Germinal Matrix	brain

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