Variant report

Variant	rs4711413
Chromosome Location	chr6:35260858-35260859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:35260740-35260890	A549	lung:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35257372..35267692-chr6:35433856..35438688,25	K562	blood:
2	chr6:35260730..35269335-chr6:35433870..35444063,22	MCF-7	breast:
3	chr6:35226889..35228758-chr6:35259523..35261436,2	MCF-7	breast:
4	chr6:35257372..35267871-chr6:35433266..35439192,25	K562	blood:
5	chr6:35227214..35229292-chr6:35260435..35263392,2	K562	blood:
6	chr6:35260813..35263112-chr6:35464822..35466518,2	K562	blood:
7	chr6:35259972..35262009-chr6:35419216..35421184,2	MCF-7	breast:
8	chr6:35260793..35263953-chr6:35263989..35266366,4	K562	blood:
9	chr6:35259383..35261485-chr6:35435927..35437799,2	MCF-7	breast:

No data

Variant related genes	Relation type
DEF6	TF binding region
ZNF76	TF binding region
ENSG00000198755	Chromatin interaction
ENSG00000065029	Chromatin interaction
ENSG00000112039	Chromatin interaction
ENSG00000007866	Chromatin interaction
ENSG00000023892	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10080361	0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1013907	0.93[ASN][1000 genomes]
rs1034449	1.00[MKK][hapmap]
rs10755687	0.88[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10807150	0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10947540	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1108709	0.81[ASN][1000 genomes]
rs1194	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12173347	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12173582	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12211765	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12211943	0.83[ASN][1000 genomes]
rs13214290	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1557567	0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1557568	0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1590381	0.81[ASN][1000 genomes]
rs16872484	0.82[AFR][1000 genomes]
rs1888822	0.82[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1888823	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1888824	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1888825	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1894650	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1894651	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1894652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894653	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]
rs1929847	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1929849	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1987673	0.89[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2006184	0.89[ASN][1000 genomes]
rs2018373	0.87[ASN][1000 genomes]
rs2032538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2057537	1.00[ASW][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs2071920	0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2183834	0.88[ASN][1000 genomes]
rs2267657	0.89[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2267658	0.93[ASN][1000 genomes]
rs2267660	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267661	0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267662	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2267663	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2267664	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2284195	0.94[ASN][1000 genomes]
rs2395614	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2395621	0.81[ASN][1000 genomes]
rs3756855	0.82[AFR][1000 genomes]
rs3777742	0.82[ASN][1000 genomes]
rs3777743	0.82[ASN][1000 genomes]
rs3777744	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs3798342	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];0.99[ASN][1000 genomes]
rs3798343	0.94[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs3800382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3800383	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];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800385	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3800386	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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800387	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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800388	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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800392	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3800393	0.80[ASN][1000 genomes]
rs3800396	0.85[ASN][1000 genomes]
rs3800398	0.85[ASN][1000 genomes]
rs3800399	0.86[ASN][1000 genomes]
rs3800400	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3823434	0.81[GIH][hapmap]
rs4583983	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711409	0.93[ASN][1000 genomes]
rs4711411	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4711414	0.94[ASN][1000 genomes]
rs4713841	0.85[ASN][1000 genomes]
rs4713845	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4713847	0.81[ASN][1000 genomes]
rs4713848	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];0.97[ASN][1000 genomes]
rs4713850	0.83[ASN][1000 genomes]
rs58925593	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62403575	0.94[ASN][1000 genomes]
rs6457812	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs68164647	0.86[ASN][1000 genomes]
rs6902523	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6907324	0.94[ASN][1000 genomes]
rs6907573	0.88[ASN][1000 genomes]
rs6907795	0.85[ASN][1000 genomes]
rs6913037	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6913475	0.81[ASN][1000 genomes]
rs6913941	0.86[ASN][1000 genomes]
rs6916364	0.86[ASN][1000 genomes]
rs6920432	0.81[ASN][1000 genomes]
rs6920747	0.94[ASN][1000 genomes]
rs6927730	0.86[ASN][1000 genomes]
rs6928769	0.91[ASN][1000 genomes]
rs6930562	0.82[ASN][1000 genomes]
rs6938946	0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6941471	0.83[ASN][1000 genomes]
rs72909061	0.91[ASN][1000 genomes]
rs7757316	0.81[ASN][1000 genomes]
rs7763946	0.92[ASN][1000 genomes]
rs7769906	0.94[ASN][1000 genomes]
rs7772212	0.94[ASN][1000 genomes]
rs8205	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs914547	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9296144	0.93[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9296150	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9348962	1.00[ASW][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs9348974	0.89[EUR][1000 genomes]
rs9357194	1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs9366882	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs9366883	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9366885	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368852	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9368853	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9368854	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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9368857	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];0.99[ASN][1000 genomes]
rs9368859	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368860	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368865	0.89[EUR][1000 genomes]
rs9368868	0.81[GIH][hapmap]
rs9380491	1.00[CEU][hapmap]
rs9380492	1.00[ASW][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs9380498	0.86[ASN][1000 genomes]
rs9380500	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9380501	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9380502	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380505	0.89[EUR][1000 genomes]
rs9380507	0.89[EUR][1000 genomes]
rs9394283	0.92[ASN][1000 genomes]
rs9394288	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9394289	0.94[ASN][1000 genomes]
rs9462065	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9462072	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9469964	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9469972	0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs9469975	0.84[ASN][1000 genomes]
rs9469979	0.93[ASN][1000 genomes]
rs9469982	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs9469997	0.83[ASN][1000 genomes]
rs9469998	0.81[ASN][1000 genomes]
rs965272	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs968828	0.81[ASN][1000 genomes]
rs975496	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs991145	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4711413	DEF6	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35232600-35265200	Weak transcription	Stomach Mucosa	stomach
2	chr6:35237800-35264800	Weak transcription	K562	blood
3	chr6:35243400-35265000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:35247800-35264600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:35248000-35264800	Strong transcription	Stomach Smooth Muscle	stomach
6	chr6:35248400-35262200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr6:35248400-35263400	Strong transcription	Rectal Smooth Muscle	rectum
8	chr6:35248400-35264400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:35248600-35264200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr6:35248600-35264200	Strong transcription	Fetal Thymus	thymus
11	chr6:35248600-35264400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr6:35248800-35261200	Weak transcription	A549	lung
13	chr6:35248800-35262000	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:35248800-35263600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:35248800-35263600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr6:35248800-35263800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:35248800-35264000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:35248800-35264000	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:35248800-35264000	Strong transcription	Dnd41	blood
20	chr6:35248800-35264200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:35248800-35264400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:35248800-35264400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:35248800-35264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:35248800-35264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:35248800-35264600	Strong transcription	Primary T cells from cord blood	blood
26	chr6:35248800-35264600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:35248800-35264800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:35248800-35264800	Strong transcription	Thymus	Thymus
29	chr6:35248800-35265000	Strong transcription	Fetal Intestine Small	intestine
30	chr6:35248800-35265000	Strong transcription	Fetal Stomach	stomach
31	chr6:35248800-35265400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:35248800-35265800	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr6:35249000-35263400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:35249000-35264200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr6:35249000-35264600	Strong transcription	Brain Anterior Caudate	brain
36	chr6:35249000-35264600	Strong transcription	Brain Cingulate Gyrus	brain
37	chr6:35249000-35264600	Strong transcription	Fetal Intestine Large	intestine
38	chr6:35249000-35265000	Strong transcription	Liver	Liver
39	chr6:35249000-35265200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:35249000-35265200	Strong transcription	Osteobl	bone
41	chr6:35249000-35265400	Weak transcription	Right Atrium	heart
42	chr6:35249000-35266800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:35249200-35264400	Strong transcription	Placenta	Placenta
44	chr6:35249200-35265400	Strong transcription	Fetal Brain Female	brain
45	chr6:35249400-35263600	Strong transcription	Aorta	Aorta
46	chr6:35250000-35263400	Strong transcription	Brain Angular Gyrus	brain
47	chr6:35250000-35263600	Strong transcription	GM12878-XiMat	blood
48	chr6:35250200-35261400	Strong transcription	Pancreas	Pancrea
49	chr6:35251000-35264400	Strong transcription	Adipose Nuclei	Adipose
50	chr6:35251000-35266800	Weak transcription	Fetal Brain Male	brain

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