Variant report

Variant	rs27090
Chromosome Location	chr5:61698663-61698664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr5:61698279-61698717	GM12878	blood:	n/a	n/a
2	ATF2	chr5:61698223-61698688	GM12878	blood:	n/a	n/a
3	ATF2	chr5:61698225-61698704	GM12878	blood:	n/a	n/a
4	MYC	chr5:61698567-61700315	A549	lung:	n/a	chr5:61700046-61700062
5	MXI1	chr5:61698524-61700344	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr5:61697820-61700282	MCF10A-Er-Src	breast:	n/a	n/a
7	MEF2A	chr5:61698313-61698668	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:61697842-61700273	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr5:61698645-61698675	HepG2	liver:	n/a	n/a
10	MYC	chr5:61698414-61700039	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:72519248..72520809-chr5:61697872..61699713,2	MCF-7	breast:
2	chr5:61685307..61687523-chr5:61697635..61699406,2	K562	blood:
3	chr5:61686012..61687975-chr5:61698243..61700042,2	MCF-7	breast:
4	chr5:61696503..61703698-chr5:61706632..61711868,15	MCF-7	breast:
5	chr5:61601759..61603415-chr5:61698105..61699743,2	K562	blood:
6	chr5:61696900..61702493-chr5:61705289..61710261,23	K562	blood:
7	chr5:61679991..61682016-chr5:61697548..61699312,2	MCF-7	breast:
8	chr5:61601492..61604171-chr5:61697960..61699657,3	K562	blood:
9	chr5:61697532..61701694-chr5:61703408..61710603,12	MCF-7	breast:
10	chr5:61686508..61688949-chr5:61697910..61699480,2	MCF-7	breast:
11	chr5:61601958..61603491-chr5:61698096..61700949,2	MCF-7	breast:
12	chr5:61571856..61574619-chr5:61696505..61699367,2	K562	blood:

No data

Variant related genes	Relation type
IPO11	TF binding region
ENSG00000086200	Chromatin interaction
ENSG00000086189	Chromatin interaction
ENSG00000068796	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1108158	0.90[CHB][hapmap]
rs11740652	0.80[ASN][1000 genomes]
rs11747516	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs12654936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12655562	0.80[ASN][1000 genomes]
rs13155253	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs13156073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs13156695	0.80[ASN][1000 genomes]
rs13174779	0.80[ASN][1000 genomes]
rs13189446	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs13190153	0.87[ASN][1000 genomes]
rs153859	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153864	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs153873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16875037	0.80[ASN][1000 genomes]
rs16890613	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs16890618	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs16890628	0.80[ASN][1000 genomes]
rs16890634	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs16890651	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs173530	0.86[ASN][1000 genomes]
rs17382217	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs181784	0.89[ASN][1000 genomes]
rs187624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2272291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs2441115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs246198	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs246200	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2463079	0.86[ASN][1000 genomes]
rs247477	0.89[ASN][1000 genomes]
rs247480	0.86[ASN][1000 genomes]
rs247481	0.89[ASN][1000 genomes]
rs247484	0.80[ASN][1000 genomes]
rs255391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs255392	0.80[ASN][1000 genomes]
rs2650500	0.81[ASN][1000 genomes]
rs26619	0.89[ASN][1000 genomes]
rs26620	0.86[ASN][1000 genomes]
rs26626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs26627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs32047	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs32053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs32148	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs32149	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs32151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs32152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs32153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs32162	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs32165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs32170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs32177	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs32178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs32180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs32183	0.81[ASN][1000 genomes]
rs32184	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs32185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs32189	0.81[ASN][1000 genomes]
rs34220654	0.80[ASN][1000 genomes]
rs34596001	0.80[ASN][1000 genomes]
rs35011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs35012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35054	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35055	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35238667	0.80[ASN][1000 genomes]
rs35572300	0.80[ASN][1000 genomes]
rs35699711	0.80[ASN][1000 genomes]
rs369624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3776612	0.80[ASN][1000 genomes]
rs3776614	0.80[ASN][1000 genomes]
rs3822487	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs40109	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs417822	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4289514	0.80[ASN][1000 genomes]
rs7446543	0.80[ASN][1000 genomes]
rs785665	0.86[ASN][1000 genomes]
rs785666	0.86[ASN][1000 genomes]
rs785667	0.86[ASN][1000 genomes]
rs814169	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs971965	0.90[CHB][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	esv2757117	chr5:61649403-61748912	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	esv35035	chr5:61657943-61792243	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs27090	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61642600-61699200	Weak transcription	Gastric	stomach
2	chr5:61665400-61699000	Weak transcription	Esophagus	oesophagus
3	chr5:61676800-61699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:61682200-61699000	Weak transcription	Colonic Mucosa	Colon
5	chr5:61690400-61698800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:61690400-61699000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:61690400-61699000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:61690600-61698800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:61696800-61699000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:61697000-61699000	Weak transcription	Placenta	Placenta
11	chr5:61697200-61698800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:61697200-61698800	Weak transcription	Thymus	Thymus
13	chr5:61697200-61699000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:61697200-61699000	Weak transcription	Fetal Thymus	thymus
15	chr5:61697200-61699000	Weak transcription	Left Ventricle	heart
16	chr5:61697200-61699000	Weak transcription	Lung	lung
17	chr5:61697200-61699200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:61697200-61699200	Weak transcription	Spleen	Spleen
19	chr5:61697400-61699000	Weak transcription	Pancreas	Pancrea
20	chr5:61697400-61699200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:61697800-61698800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:61697800-61698800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:61697800-61698800	Enhancers	Colon Smooth Muscle	Colon
24	chr5:61697800-61698800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr5:61697800-61699000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:61697800-61700800	Active TSS	NHLF	lung
27	chr5:61698000-61698800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:61698000-61698800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr5:61698000-61698800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr5:61698000-61698800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:61698000-61698800	Enhancers	Brain Anterior Caudate	brain
32	chr5:61698000-61698800	Enhancers	Fetal Intestine Small	intestine
33	chr5:61698000-61698800	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:61698000-61698800	Flanking Active TSS	A549	lung
35	chr5:61698000-61698800	Flanking Active TSS	Osteobl	bone
36	chr5:61698000-61699000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr5:61698000-61699400	Active TSS	Right Atrium	heart
38	chr5:61698000-61700200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:61698000-61700800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr5:61698000-61700800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:61698000-61700800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:61698200-61698800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:61698200-61698800	Enhancers	Primary hematopoietic stem cells	blood
44	chr5:61698200-61698800	Enhancers	Adipose Nuclei	Adipose
45	chr5:61698200-61698800	Enhancers	Brain Angular Gyrus	brain
46	chr5:61698200-61698800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr5:61698200-61698800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr5:61698200-61698800	Enhancers	Fetal Intestine Large	intestine
49	chr5:61698200-61698800	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr5:61698200-61698800	Flanking Active TSS	HUVEC	blood vessel

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