Variant report

Variant	rs3822485
Chromosome Location	chr5:61605063-61605064
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	ARID3A	chr5:61604107-61605112	K562	blood:	n/a	n/a
2	SPI1	chr5:61604974-61605416	HL-60	blood:	n/a	chr5:61605364-61605373 chr5:61605359-61605366
3	SPI1	chr5:61604997-61605258	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:61604944..61606842-chr5:61609048..61611891,3	MCF-7	breast:
2	chr5:61604639..61607587-chr5:61647579..61650088,2	MCF-7	breast:
3	chr5:61592874..61595599-chr5:61604099..61606788,3	K562	blood:
4	chr5:61591991..61594374-chr5:61603392..61605599,2	K562	blood:

Variant related genes	Relation type
KIF2A	TF binding region

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10062387	0.82[CHB][hapmap]
rs10069745	0.96[CEU][hapmap];0.91[CHB][hapmap]
rs10069988	0.82[CHB][hapmap];0.90[CHD][hapmap];0.80[MEX][hapmap]
rs10071537	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs101091	0.82[CHB][hapmap]
rs10461472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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]
rs10471545	0.88[CEU][hapmap];0.83[MEX][hapmap]
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]
rs12659793	0.82[CHB][hapmap]
rs12659814	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs12696990	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1301064	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap]
rs1301065	0.82[CHB][hapmap]
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	1.00[CEU][hapmap];1.00[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	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs152184	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs152186	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap]
rs152187	0.84[CEU][hapmap]
rs152191	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs152192	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.89[TSI][hapmap]
rs152199	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs152209	0.81[EUR][1000 genomes]
rs152215	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs153857	0.84[CEU][hapmap]
rs153858	0.84[CEU][hapmap]
rs153862	0.84[CEU][hapmap]
rs16890622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs173522	0.84[CEU][hapmap]
rs174647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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]
rs1995782	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs2034240	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2289883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2344396	0.88[CEU][hapmap];0.83[MEX][hapmap]
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]
rs247229	0.84[CEU][hapmap]
rs247231	0.82[CHB][hapmap]
rs247233	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs247237	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs247240	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs247244	0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs247245	0.84[CEU][hapmap]
rs247247	0.84[CEU][hapmap]
rs247250	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs247255	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247264	0.82[CHB][hapmap];0.83[YRI][hapmap]
rs247265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][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]
rs247479	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap]
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	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][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]
rs26624	0.84[CEU][hapmap]
rs26625	0.84[CEU][hapmap]
rs26628	0.84[CEU][hapmap]
rs26629	0.83[CEU][hapmap]
rs26630	0.84[CEU][hapmap]
rs26635	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap]
rs26637	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs26638	0.84[CEU][hapmap]
rs26642	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap]
rs26645	0.84[CEU][hapmap]
rs27448	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs27542	0.84[CEU][hapmap]
rs27693	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs27931	0.81[CHB][hapmap]
rs35010	0.84[CEU][hapmap]
rs35059	0.84[CEU][hapmap]
rs35119	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap]
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]
rs3846467	0.82[CHB][hapmap]
rs4145851	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs438143	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4441833	1.00[CEU][hapmap];1.00[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	0.88[CEU][hapmap]
rs4700006	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]
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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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]
rs784916	0.82[CHB][hapmap];0.84[CHD][hapmap];0.83[MEX][hapmap]
rs784921	0.96[CEU][hapmap];0.91[CHB][hapmap]
rs9291756	0.88[CEU][hapmap]
rs9291758	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs959899	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3822485	DIMT1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61603200-61629200	Weak transcription	Lung	lung
2	chr5:61603200-61629200	Weak transcription	Spleen	Spleen
3	chr5:61603400-61606800	Weak transcription	Small Intestine	intestine
4	chr5:61603400-61607400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:61603400-61625200	Weak transcription	Stomach Mucosa	stomach
6	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
7	chr5:61603600-61622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:61603600-61622400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:61603600-61629200	Weak transcription	Psoas Muscle	Psoas
10	chr5:61603800-61605200	Enhancers	Primary hematopoietic stem cells	blood
11	chr5:61603800-61605600	Enhancers	Brain Substantia Nigra	brain
12	chr5:61603800-61605800	Enhancers	Brain Angular Gyrus	brain
13	chr5:61603800-61606400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:61603800-61607600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:61603800-61607800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:61603800-61609600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:61603800-61611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:61603800-61611200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:61603800-61611200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:61603800-61629200	Weak transcription	Left Ventricle	heart
21	chr5:61604000-61605200	Weak transcription	Fetal Heart	heart
22	chr5:61604000-61605200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:61604000-61606200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:61604000-61606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:61604000-61606400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:61604000-61606400	Weak transcription	Fetal Lung	lung
27	chr5:61604000-61606400	Weak transcription	Osteobl	bone
28	chr5:61604000-61606800	Weak transcription	Adipose Nuclei	Adipose
29	chr5:61604000-61607400	Weak transcription	Fetal Intestine Small	intestine
30	chr5:61604000-61607400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:61604000-61607800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:61604000-61607800	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:61604000-61608000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:61604000-61611000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr5:61604000-61617400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr5:61604000-61622200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:61604000-61622200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:61604000-61622200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:61604000-61629000	Weak transcription	Thymus	Thymus
40	chr5:61604200-61606200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:61604200-61607000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:61604200-61609000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:61604200-61609000	Enhancers	Brain Anterior Caudate	brain
44	chr5:61604200-61609200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:61604200-61616800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:61604400-61605200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:61604400-61605400	Strong transcription	HSMM	muscle
48	chr5:61604400-61605400	Weak transcription	NH-A	brain
49	chr5:61604400-61605600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr5:61604400-61605600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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