Variant report

Variant	rs10916130
Chromosome Location	chr1:227558142-227558143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227503449..227507598-chr1:227555312..227559428,5	K562	blood:
2	chr1:227503449..227507598-chr1:227555312..227559110,4	K562	blood:
3	chr1:227506214..227507997-chr1:227555860..227558711,2	MCF-7	breast:
4	chr1:227545277..227548710-chr1:227557152..227561579,4	K562	blood:
5	chr1:227544961..227546777-chr1:227556862..227559703,3	K562	blood:
6	chr1:227556870..227561275-chr1:227563192..227568675,6	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10799414	0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10916137	0.86[ASN][1000 genomes]
rs10916138	0.86[ASN][1000 genomes]
rs1495850	1.00[JPT][hapmap]
rs55785556	0.86[ASN][1000 genomes]
rs61833063	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61833064	0.91[ASN][1000 genomes]
rs61833065	0.86[ASN][1000 genomes]
rs61833066	0.86[ASN][1000 genomes]
rs6664147	0.90[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10916130	LEFTY1	cis	parietal	SCAN
rs10916130	CDC42BPA	cis	cerebellum	SCAN
rs10916130	CDC42BPA	cis	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227545800-227571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:227556600-227559200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:227556800-227558400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:227556800-227559000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:227556800-227560800	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr1:227556800-227560800	Enhancers	Stomach Mucosa	stomach
7	chr1:227556800-227561200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:227556800-227561200	Enhancers	HUVEC	blood vessel
9	chr1:227557000-227558600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr1:227557000-227558600	Enhancers	HSMM	muscle
11	chr1:227557000-227558800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:227557000-227559000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:227557200-227558200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:227557200-227558400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:227557200-227559600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:227557200-227565400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:227557400-227558400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:227557800-227558200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:227557800-227558800	Enhancers	Osteobl	bone
20	chr1:227557800-227559000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:227558000-227558200	Flanking Active TSS	K562	blood
22	chr1:227558000-227558600	Enhancers	HSMMtube	muscle
23	chr1:227558000-227558800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:227558000-227559000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:227558000-227560600	Enhancers	A549	lung

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