Variant report

Variant	rs4700006
Chromosome Location	chr5:61604204-61604205
allele	A/C
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	EP300	chr5:61604201-61604622	K562	blood:	n/a	n/a
2	ARID3A	chr5:61604107-61605112	K562	blood:	n/a	n/a
3	POLR2A	chr5:61604113-61604260	MCF10A-Er-Src	breast:	n/a	n/a
4	EBF1	chr5:61604127-61604611	GM12878	blood:	n/a	n/a
5	CEBPB	chr5:61604199-61604704	K562	blood:	n/a	chr5:61604510-61604521
6	POLR2A	chr5:61603841-61604746	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:61592874..61595599-chr5:61604099..61606788,3	K562	blood:
2	chr5:61601799..61604714-chr5:61698844..61701505,2	MCF-7	breast:
3	chr5:61591991..61594374-chr5:61603392..61605599,2	K562	blood:

Variant related genes	Relation type
KIF2A	TF binding region
ENSG00000086200	Chromatin interaction
ENSG00000086189	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10069745	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs10071537	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10461472	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10471546	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939937	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12515967	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12696990	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1309156	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13155700	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361143	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13361219	0.83[ASN][1000 genomes]
rs149540	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs152184	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs152191	0.87[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs152192	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs152199	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs152209	0.81[EUR][1000 genomes]
rs152215	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs16890622	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs174647	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2034240	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2289883	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247218	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247220	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247221	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247222	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247223	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247233	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs247240	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs247244	0.87[CEU][hapmap]
rs247255	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247264	0.82[YRI][hapmap]
rs247265	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247267	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247268	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247269	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247270	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs247273	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247275	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs264519	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs264520	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs264521	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs264523	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs264528	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs264530	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs264531	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26637	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs27693	0.87[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs35348760	0.83[ASN][1000 genomes]
rs3776615	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3822485	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145851	0.83[ASN][1000 genomes]
rs438143	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4441833	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700004	0.84[CEU][hapmap]
rs4700009	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56836756	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67150497	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7700569	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7702634	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7707035	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs784921	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs9291756	0.84[CEU][hapmap]
rs9291758	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs959899	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9968583	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968586	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv830318	chr5:61415713-61623320	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv2755585	chr5:61535831-61618595	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61601200-61604400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:61601600-61604400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr5:61601800-61604400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:61601800-61604400	Active TSS	NH-A	brain
5	chr5:61601800-61604400	Active TSS	NHLF	lung
6	chr5:61602800-61604600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:61602800-61604600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:61603000-61604600	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr5:61603200-61604600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr5:61603200-61629200	Weak transcription	Lung	lung
11	chr5:61603200-61629200	Weak transcription	Spleen	Spleen
12	chr5:61603400-61604400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr5:61603400-61604400	Enhancers	Pancreas	Pancrea
14	chr5:61603400-61604600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr5:61603400-61606800	Weak transcription	Small Intestine	intestine
16	chr5:61603400-61607400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:61603400-61625200	Weak transcription	Stomach Mucosa	stomach
18	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
19	chr5:61603600-61604400	Enhancers	Liver	Liver
20	chr5:61603600-61604400	Enhancers	Esophagus	oesophagus
21	chr5:61603600-61604400	Enhancers	Fetal Muscle Leg	muscle
22	chr5:61603600-61604600	Enhancers	Primary B cells from peripheral blood	blood
23	chr5:61603600-61622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:61603600-61622400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:61603600-61629200	Weak transcription	Psoas Muscle	Psoas
26	chr5:61603800-61604400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:61603800-61604400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:61603800-61604400	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr5:61603800-61604400	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr5:61603800-61604400	Weak transcription	Colonic Mucosa	Colon
31	chr5:61603800-61604400	Flanking Active TSS	Fetal Brain Female	brain
32	chr5:61603800-61604400	Enhancers	Fetal Intestine Large	intestine
33	chr5:61603800-61604400	Transcr. at gene 5' and 3'	HMEC	breast
34	chr5:61603800-61604400	Flanking Active TSS	NHDF-Ad	bronchial
35	chr5:61603800-61604600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr5:61603800-61604600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr5:61603800-61604600	Transcr. at gene 5' and 3'	Dnd41	blood
38	chr5:61603800-61604600	Enhancers	HepG2	liver
39	chr5:61603800-61604600	Transcr. at gene 5' and 3'	K562	blood
40	chr5:61603800-61604800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr5:61603800-61605200	Enhancers	Primary hematopoietic stem cells	blood
42	chr5:61603800-61605600	Enhancers	Brain Substantia Nigra	brain
43	chr5:61603800-61605800	Enhancers	Brain Angular Gyrus	brain
44	chr5:61603800-61606400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:61603800-61607600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr5:61603800-61607800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr5:61603800-61609600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:61603800-61611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:61603800-61611200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr5:61603800-61611200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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