Variant report

Variant	rs2910474
Chromosome Location	chr5:61440321-61440322
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	CTCF	chr5:61440220-61440370	AG09309	skin:	n/a	n/a
2	FOS	chr5:61440311-61440536	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr5:61440180-61440330	AG04449	skin:	n/a	n/a

Variant related genes	Relation type
RN7SKP157	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11953146	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1508893	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812798	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1960456	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2017818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910476	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940579	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940586	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2940591	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2961836	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2961837	1.00[CEU][hapmap];1.00[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];0.98[ASN][1000 genomes]
rs2962027	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2962030	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235491	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4498216	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700472	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55947343	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7712470	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv830317	chr5:61298840-61478113	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1022497	chr5:61424594-61470438	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1026425	chr5:61424594-61471448	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1025920	chr5:61424594-61471782	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2763457	chr5:61424606-61472050	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1017594	chr5:61425095-61471448	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv598322	chr5:61428137-61452417	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv462201	chr5:61428137-61461609	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv471014	chr5:61428137-61461609	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv598323	chr5:61428137-61461609	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv462202	chr5:61430431-61461609	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv598324	chr5:61430431-61461609	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv598325	chr5:61436505-61468051	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2910474	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61435000-61441600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:61437800-61440600	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr5:61438000-61440400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr5:61438000-61440600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:61438200-61440400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr5:61438200-61440800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr5:61438400-61440400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr5:61438600-61440800	Enhancers	Brain Substantia Nigra	brain
9	chr5:61438800-61440800	Enhancers	Brain Anterior Caudate	brain
10	chr5:61439000-61440800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:61439200-61440400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:61439200-61440400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
13	chr5:61439200-61440600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:61439200-61440600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
15	chr5:61439200-61441000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:61439200-61441000	Enhancers	Fetal Brain Male	brain
17	chr5:61439400-61440400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:61439400-61440400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:61439400-61440600	Enhancers	Fetal Lung	lung
20	chr5:61439400-61440600	Active TSS	Stomach Smooth Muscle	stomach
21	chr5:61439400-61440800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:61439400-61440800	Enhancers	NH-A	brain
23	chr5:61439400-61441000	Enhancers	NHEK	skin
24	chr5:61439400-61441200	Enhancers	HMEC	breast
25	chr5:61439600-61440400	Enhancers	Adipose Nuclei	Adipose
26	chr5:61439600-61440600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:61439600-61440800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:61439800-61440400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
29	chr5:61439800-61440400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr5:61439800-61440400	Enhancers	Stomach Mucosa	stomach
31	chr5:61439800-61440600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:61439800-61440800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr5:61439800-61440800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:61439800-61440800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:61439800-61440800	Enhancers	Pancreas	Pancrea
36	chr5:61440000-61440400	Enhancers	Aorta	Aorta
37	chr5:61440000-61440400	Bivalent Enhancer	HUVEC	blood vessel
38	chr5:61440000-61440600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:61440000-61440600	Enhancers	Brain Angular Gyrus	brain
40	chr5:61440000-61440600	Enhancers	Brain Hippocampus Middle	brain
41	chr5:61440000-61440800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr5:61440000-61441000	Enhancers	Osteobl	bone
43	chr5:61440200-61440400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr5:61440200-61440600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:61440200-61440600	Enhancers	Fetal Brain Female	brain
46	chr5:61440200-61440800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:61440200-61440800	Enhancers	Brain Cingulate Gyrus	brain
48	chr5:61440200-61440800	Enhancers	Brain Germinal Matrix	brain

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