Variant report

Variant	rs2279465
Chromosome Location	chr11:46399538-46399539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:46399537-46406317	K562	blood:	n/a	n/a
2	POLR2A	chr11:46398695-46401456	HL-60	blood:	n/a	n/a
3	POLR2A	chr11:46399047-46401518	K562	blood:	n/a	n/a
4	ZNF143	chr11:46399533-46399705	K562	blood:	n/a	n/a
5	CBX3	chr11:46399359-46399798	K562	blood:	n/a	n/a
6	POLR2A	chr11:46399455-46399647	HUVEC	blood vessel:	n/a	n/a
7	USF2	chr11:46399522-46399669	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:46399298-46399960	Hela-S3	cervix:	n/a	n/a
9	TRIM28	chr11:46399449-46399795	K562	blood:	n/a	n/a
10	POLR2A	chr11:46398742-46401481	HL-60	blood:	n/a	n/a
11	POLR2A	chr11:46398748-46401609	K562	blood:	n/a	n/a
12	POLR2A	chr11:46399194-46401040	K562	blood:	n/a	n/a
13	CBX3	chr11:46399430-46399768	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:46367411..46370383-chr11:46395468..46399934,4	K562	blood:
2	chr11:46399063..46400618-chr11:46400770..46402809,2	MCF-7	breast:
3	chr11:46256874..46260563-chr11:46399060..46405748,9	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MDK-2	chr11:46399520-46399779	NONHSAT021173

No data

Variant related genes	Relation type
MDK	TF binding region
ENSG00000254639	Chromatin interaction
ENSG00000149091	Chromatin interaction
ENSG00000110492	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10160701	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs10838602	0.96[EUR][1000 genomes]
rs11038897	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11038900	0.96[EUR][1000 genomes]
rs11038906	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs11038914	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs11038919	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11038927	0.94[EUR][1000 genomes]
rs11819869	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12272795	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs12283172	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12292425	0.92[EUR][1000 genomes]
rs12295266	0.93[EUR][1000 genomes]
rs12573978	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12574250	1.00[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12574668	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12575519	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576115	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576317	0.98[EUR][1000 genomes]
rs12576359	0.96[EUR][1000 genomes]
rs12577142	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578042	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1472001	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs1489192	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs16938506	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17197116	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2046768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs2067482	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2171667	1.00[CEU][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes]
rs2171668	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2291487	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2864072	0.98[EUR][1000 genomes]
rs2864076	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2902858	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs34406563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35324223	0.86[EUR][1000 genomes]
rs35623865	0.91[EUR][1000 genomes]
rs3740974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802888	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3809047	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4307676	0.87[EUR][1000 genomes]
rs55657382	0.91[EUR][1000 genomes]
rs55661562	0.91[EUR][1000 genomes]
rs57535407	0.98[EUR][1000 genomes]
rs58147945	0.96[EUR][1000 genomes]
rs59319338	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60722866	0.88[EUR][1000 genomes]
rs60932698	0.89[EUR][1000 genomes]
rs61882674	0.84[EUR][1000 genomes]
rs61882678	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882682	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882683	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882691	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61882701	0.98[EUR][1000 genomes]
rs61882702	0.98[EUR][1000 genomes]
rs61882706	0.97[EUR][1000 genomes]
rs61882709	0.98[EUR][1000 genomes]
rs61882710	0.98[EUR][1000 genomes]
rs61882711	0.98[EUR][1000 genomes]
rs61882712	0.96[EUR][1000 genomes]
rs61882720	0.95[EUR][1000 genomes]
rs61882743	0.94[EUR][1000 genomes]
rs61882746	0.97[EUR][1000 genomes]
rs61882748	0.98[EUR][1000 genomes]
rs61882750	0.97[EUR][1000 genomes]
rs61882756	0.91[EUR][1000 genomes]
rs61882757	0.93[EUR][1000 genomes]
rs61882758	0.93[EUR][1000 genomes]
rs61884262	0.85[EUR][1000 genomes]
rs61884264	0.91[EUR][1000 genomes]
rs61884271	0.89[EUR][1000 genomes]
rs61884273	0.87[EUR][1000 genomes]
rs61884274	0.87[EUR][1000 genomes]
rs6485682	1.00[CEU][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes]
rs6485685	0.91[EUR][1000 genomes]
rs7108770	0.89[EUR][1000 genomes]
rs7109698	0.83[EUR][1000 genomes]
rs7112229	0.93[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7122039	0.92[EUR][1000 genomes]
rs7125907	0.92[EUR][1000 genomes]
rs7126316	0.86[EUR][1000 genomes]
rs7126343	0.87[EUR][1000 genomes]
rs7127529	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7128092	0.86[EUR][1000 genomes]
rs7130141	0.87[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs73449983	0.93[EUR][1000 genomes]
rs7481312	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7484002	0.91[EUR][1000 genomes]
rs7924401	0.92[EUR][1000 genomes]
rs7930103	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs7932866	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs7936413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7946705	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7951579	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7951870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs876701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv554201	chr11:46281835-46422686	Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv825867	chr11:46303184-46425613	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1797501	chr11:46315437-46402521	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	esv1811345	chr11:46317062-46438072	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv554202	chr11:46334239-46469900	Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv897316	chr11:46349631-46417815	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription 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 miRNA	20 gene(s)	inside rSNPs	diseases
7	nsv897317	chr11:46363411-46417815	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
8	nsv897318	chr11:46388220-46417815	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv897319	chr11:46396479-46417815	Genic enhancers Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	nsv554203	chr11:46399538-46406497	Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2279465	ATG13	cis	parietal	SCAN
rs2279465	C11orf49	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46383600-46402000	Weak transcription	Fetal Brain Male	brain
2	chr11:46385200-46400600	Strong transcription	Thymus	Thymus
3	chr11:46385400-46401200	Strong transcription	Dnd41	blood
4	chr11:46386000-46402200	Weak transcription	NHDF-Ad	bronchial
5	chr11:46388600-46400200	Strong transcription	Gastric	stomach
6	chr11:46388800-46400600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:46389000-46399600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:46389000-46399600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:46389000-46402000	Weak transcription	Right Atrium	heart
10	chr11:46389400-46400200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:46389400-46400400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr11:46389400-46401400	Strong transcription	Primary T cells from cord blood	blood
13	chr11:46389600-46399800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:46389600-46400200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:46389600-46400200	Strong transcription	Liver	Liver
16	chr11:46389600-46400200	Strong transcription	Left Ventricle	heart
17	chr11:46389600-46400200	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:46389600-46400400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr11:46389600-46400400	Strong transcription	Adipose Nuclei	Adipose
20	chr11:46389600-46400400	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr11:46389600-46401200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:46389600-46401800	Weak transcription	Stomach Mucosa	stomach
23	chr11:46389800-46400000	Strong transcription	Pancreas	Pancrea
24	chr11:46389800-46400200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:46389800-46400200	Strong transcription	Brain Cingulate Gyrus	brain
26	chr11:46389800-46400600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:46389800-46401000	Strong transcription	Fetal Thymus	thymus
28	chr11:46390000-46399600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:46390000-46400000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr11:46390200-46400000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:46390200-46400400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:46390200-46401200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:46391000-46399800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:46391000-46402000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:46391200-46400400	Strong transcription	Fetal Brain Female	brain
36	chr11:46391400-46400400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:46391400-46400600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:46391400-46402200	Weak transcription	NH-A	brain
39	chr11:46391600-46399800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:46391600-46400200	Strong transcription	Brain Germinal Matrix	brain
41	chr11:46391600-46400200	Strong transcription	NHLF	lung
42	chr11:46391600-46400400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:46391600-46400600	Weak transcription	Hela-S3	cervix
44	chr11:46391600-46400800	Weak transcription	K562	blood
45	chr11:46391800-46399800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:46391800-46399800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr11:46391800-46399800	Weak transcription	HepG2	liver
48	chr11:46391800-46400000	Strong transcription	Brain Hippocampus Middle	brain
49	chr11:46391800-46400200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:46391800-46400400	Strong transcription	Primary T cells fromperipheralblood	blood

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