Variant report

Variant	rs656753
Chromosome Location	chr1:210468504-210468505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210428073..210429613-chr1:210467774..210469897,2	MCF-7	breast:
2	chr1:210467132..210470101-chr1:210476675..210478835,2	MCF-7	breast:
3	chr1:210418192..210421005-chr1:210465903..210469381,6	MCF-7	breast:
4	chr1:210467411..210469958-chr1:210471110..210473541,2	K562	blood:
5	chr1:210466185..210468740-chr1:210546709..210548670,2	MCF-7	breast:
6	chr1:210468377..210470093-chr1:210472227..210474687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction
ENSG00000233455	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1040563	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12739013	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12739023	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1338285	0.80[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs4314881	0.84[GIH][hapmap]
rs4844990	0.93[AFR][1000 genomes]
rs655829	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655847	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658075	0.95[ASN][1000 genomes]
rs669189	0.92[AFR][1000 genomes]
rs670441	0.94[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs656753	SYT14	cis	parietal	SCAN
rs656753	SERTAD4	cis	parietal	SCAN
rs656753	HHAT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210465800-210470200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:210466400-210468800	Enhancers	Duodenum Mucosa	Duodenum
3	chr1:210466400-210468800	Enhancers	Stomach Mucosa	stomach
4	chr1:210466400-210469400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:210466600-210469000	Enhancers	NHLF	lung
6	chr1:210466600-210469200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:210466600-210469600	Enhancers	Rectal Smooth Muscle	rectum
8	chr1:210466600-210470000	Enhancers	Fetal Stomach	stomach
9	chr1:210466600-210474200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:210466800-210469200	Enhancers	Colon Smooth Muscle	Colon
11	chr1:210466800-210469400	Enhancers	Adipose Nuclei	Adipose
12	chr1:210466800-210469400	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr1:210466800-210477400	Enhancers	Fetal Muscle Leg	muscle
14	chr1:210467000-210468600	Weak transcription	HSMM	muscle
15	chr1:210467000-210468800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:210467000-210469400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:210467000-210470000	Enhancers	Fetal Muscle Trunk	muscle
18	chr1:210467200-210468600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:210467200-210469000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:210467200-210469400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:210467200-210469400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:210467200-210469800	Enhancers	Fetal Heart	heart
23	chr1:210467200-210470000	Weak transcription	Fetal Kidney	kidney
24	chr1:210467400-210469200	Enhancers	Aorta	Aorta
25	chr1:210467600-210468600	Enhancers	Lung	lung
26	chr1:210467600-210468800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:210467600-210469000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
28	chr1:210467600-210469200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:210467600-210469200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:210467800-210468800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:210467800-210468800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr1:210467800-210468800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
33	chr1:210467800-210469000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:210467800-210469000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:210467800-210469200	Enhancers	Placenta	Placenta
36	chr1:210467800-210469400	Enhancers	Fetal Lung	lung
37	chr1:210467800-210469400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:210468000-210468600	Enhancers	H9 Cell Line	embryonic stem cell
39	chr1:210468000-210468600	Enhancers	Brain Substantia Nigra	brain
40	chr1:210468000-210468600	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr1:210468000-210468600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:210468000-210468800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:210468000-210468800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:210468000-210468800	Enhancers	Brain Hippocampus Middle	brain
45	chr1:210468000-210468800	Enhancers	Left Ventricle	heart
46	chr1:210468000-210468800	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr1:210468000-210469000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr1:210468000-210469000	Enhancers	H1 Cell Line	embryonic stem cell
49	chr1:210468000-210469000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
50	chr1:210468000-210469000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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