Variant report

Variant	rs10796955
Chromosome Location	chr1:155959303-155959304
allele	A/G
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	ZNF143	chr1:155959194-155959537	K562	blood:	n/a	n/a
2	CHD2	chr1:155959206-155959469	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr1:155959280-155959430	GM12875	blood:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
4	CTCF	chr1:155959300-155959450	SAEC	small airway:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
5	TBL1XR1	chr1:155959173-155959594	GM12878	blood:	n/a	n/a
6	RAD21	chr1:155958961-155959703	HepG2	liver:	n/a	chr1:155959342-155959361
7	FOXM1	chr1:155959028-155959571	GM12878	blood:	n/a	n/a
8	CTCF	chr1:155958977-155959632	A549	lung:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
9	CTCF	chr1:155958749-155959839	SK-N-SH	brain:	n/a	chr1:155958914-155958927 chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
10	WRNIP1	chr1:155959162-155959886	GM12878	blood:	n/a	n/a
11	CTCF	chr1:155959280-155959430	HepG2	liver:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
12	CTCF	chr1:155959280-155959430	NHEK	skin:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
13	CTCF	chr1:155959280-155959430	RPTEC	kidney:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
14	SIN3A	chr1:155959166-155959511	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr1:155959012-155959541	GM12892	blood:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
16	RAD21	chr1:155959116-155959480	K562	blood:	n/a	chr1:155959342-155959361
17	CTCF	chr1:155959300-155959450	GM12869	blood:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
18	CTCF	chr1:155959300-155959450	GM12866	blood:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
19	CTCF	chr1:155959300-155959450	HVMF	connective:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
20	RUNX3	chr1:155959114-155959683	GM12878	blood:	n/a	n/a
21	RAD21	chr1:155958939-155959572	IMR90	lung:	n/a	chr1:155959342-155959361
22	CTCF	chr1:155959280-155959430	HPAF	blood vessel:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
23	RAD21	chr1:155959201-155959435	K562	blood:	n/a	chr1:155959342-155959361
24	FOXA2	chr1:155959214-155959431	HepG2	liver:	n/a	n/a
25	CTCF	chr1:155959051-155959511	NHEK	skin:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
26	CTCF	chr1:155959280-155959430	HRPEpiC	eye:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
27	ELF1	chr1:155959124-155959478	A549	lung:	n/a	n/a
28	CTCF	chr1:155959300-155959450	HEK293	kidney:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
29	ZC3H11A	chr1:155959255-155959423	K562	blood:	n/a	n/a
30	GTF2F1	chr1:155959148-155959509	Hela-S3	cervix:	n/a	n/a
31	RAD21	chr1:155959011-155959595	H1-hESC	embryonic stem cell:	n/a	chr1:155959342-155959361
32	CTCF	chr1:155959168-155959487	ECC-1	luminal epithelium:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
33	CTCF	chr1:155958793-155959955	A549	lung:	n/a	chr1:155958914-155958927 chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
34	MAZ	chr1:155959252-155959466	HepG2	liver:	n/a	n/a
35	CTCF	chr1:155959300-155959450	GM12864	blood:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
36	CTCF	chr1:155959280-155959430	GM12864	blood:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
37	CTCF	chr1:155959280-155959430	HA-sp	spinal cord:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
38	CTCF	chr1:155959280-155959430	GM06990	blood:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
39	RCOR1	chr1:155959198-155959477	HepG2	liver:	n/a	n/a
40	FOXM1	chr1:155959033-155959604	GM12878	blood:	n/a	n/a
41	CTCF	chr1:155959260-155959410	Hela-S3	cervix:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
42	BHLHE40	chr1:155959294-155959474	K562	blood:	n/a	n/a
43	POLR2A	chr1:155959122-155959391	HUVEC	blood vessel:	n/a	n/a
44	CTCF	chr1:155959300-155959450	GM12872	blood:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
45	ELK1	chr1:155959177-155959461	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr1:155959280-155959430	BJ	skin:	n/a	chr1:155959350-155959359 chr1:155959346-155959359 chr1:155959344-155959362 chr1:155959339-155959360
47	IRF3	chr1:155959148-155959434	GM12878	blood:	n/a	n/a
48	MYC	chr1:155959244-155959374	HUVEC	blood vessel:	n/a	n/a
49	CHD1	chr1:155959289-155959528	GM12878	blood:	n/a	n/a
50	MYC	chr1:155959228-155959399	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155935914..155936891-chr1:155958874..155959697,4	MCF-7	breast:
2	chr1:155958637..155961186-chr1:155975621..155978419,3	MCF-7	breast:
3	chr1:155902871..155906324-chr1:155958036..155960843,4	K562	blood:
4	chr1:155903740..155906324-chr1:155958823..155960843,2	K562	blood:
5	chr1:155931505..155932309-chr1:155959250..155959861,3	MCF-7	breast:
6	chr1:155946653..155948454-chr1:155959056..155961851,2	K562	blood:
7	chr1:155902685..155905586-chr1:155957752..155961229,4	MCF-7	breast:
8	chr1:155935970..155939693-chr1:155959127..155962229,3	K562	blood:
9	chr1:155931401..155932387-chr1:155958715..155959801,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224276	TF binding region
ARHGEF2	TF binding region
ENSG00000132680	Chromatin interaction
ENSG00000116584	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10908483	0.80[AMR][1000 genomes]
rs1111102	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs11264422	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11264426	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11585845	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12026057	0.84[AMR][1000 genomes]
rs12037177	0.95[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs12118795	0.81[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12144175	0.81[AMR][1000 genomes]
rs12568523	0.95[CEU][hapmap]
rs1749405	0.80[CHB][hapmap]
rs1889532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1889533	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2016251	0.95[CEU][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes]
rs2282301	0.95[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs2297649	0.95[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2364403	0.85[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs2993207	0.80[CHB][hapmap]
rs3820594	0.86[MEX][hapmap]
rs3856261	0.88[JPT][hapmap]
rs4661175	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4661217	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488079	0.80[CHB][hapmap]
rs490498	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs539602	0.80[CHB][hapmap]
rs61813286	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs625658	0.80[CHB][hapmap]
rs6427297	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs66466805	0.82[AMR][1000 genomes]
rs6667652	0.95[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes]
rs6670477	0.80[AMR][1000 genomes]
rs6670493	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696019	0.95[CEU][hapmap];0.80[AMR][1000 genomes]
rs670523	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs72708205	0.81[AMR][1000 genomes]
rs7521292	0.81[AMR][1000 genomes]
rs7534858	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7545308	0.80[AMR][1000 genomes]
rs822478	0.89[JPT][hapmap]
rs867548	0.82[AMR][1000 genomes]
rs867549	0.95[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs867550	0.95[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs915178	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs915181	0.95[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes]
rs928596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10796955	YY1AP1	cis	cerebellum	SCAN
rs10796955	RIT1	cis	cerebellum	SCAN
rs10796955	ROBLD3	cis	parietal	SCAN
rs10796955	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10796955	PRUNE	cis	cerebellum	SCAN
rs10796955	SPRR3	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155952000-155960800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:155953600-155960800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:155953800-155959400	Weak transcription	GM12878-XiMat	blood
4	chr1:155954200-155959400	Weak transcription	K562	blood
5	chr1:155954400-155960800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:155954600-155970800	Weak transcription	NHEK	skin
7	chr1:155958600-155959400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:155958600-155959400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:155958600-155959400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:155958600-155959400	Active TSS	Aorta	Aorta
11	chr1:155958600-155959400	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr1:155958600-155959400	Enhancers	Fetal Heart	heart
13	chr1:155958600-155959600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:155958600-155959600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:155958600-155959600	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr1:155958600-155959600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr1:155958600-155959600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:155958600-155959600	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr1:155958600-155960600	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:155958600-155961000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:155958600-155961600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:155958800-155959400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr1:155958800-155959400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr1:155958800-155959400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:155958800-155959400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:155958800-155959400	Enhancers	Primary B cells from cord blood	blood
27	chr1:155958800-155959400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:155958800-155959400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:155958800-155959400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:155958800-155959400	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr1:155958800-155959400	Flanking Active TSS	Colonic Mucosa	Colon
32	chr1:155958800-155959400	Flanking Active TSS	Fetal Stomach	stomach
33	chr1:155958800-155959400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr1:155958800-155959400	Enhancers	HMEC	breast
35	chr1:155958800-155959400	Flanking Active TSS	HSMM	muscle
36	chr1:155958800-155959400	Flanking Active TSS	NHDF-Ad	bronchial
37	chr1:155958800-155959400	Flanking Active TSS	NHLF	lung
38	chr1:155958800-155959400	Flanking Active TSS	Osteobl	bone
39	chr1:155958800-155959600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:155958800-155959600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:155958800-155959600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:155958800-155959600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:155958800-155959600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr1:155958800-155959600	Enhancers	Stomach Mucosa	stomach
45	chr1:155958800-155959600	Enhancers	A549	lung
46	chr1:155958800-155959800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:155958800-155959800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr1:155958800-155959800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr1:155958800-155959800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr1:155958800-155959800	Flanking Active TSS	Brain Hippocampus Middle	brain

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