Variant report

Variant	rs9393693
Chromosome Location	chr6:26277408-26277409
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	POLR2A	chr6:26277337-26277837	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:26276394-26278311	K562	blood:	n/a	n/a
3	POLR2A	chr6:26277285-26277798	K562	blood:	n/a	n/a
4	POLR2A	chr6:26277163-26278145	K562	blood:	n/a	n/a
5	POLR2A	chr6:26277345-26277834	K562	blood:	n/a	n/a
6	POLR2A	chr6:26276668-26277873	K562	blood:	n/a	n/a
7	POLR2A	chr6:26277197-26277634	K562	blood:	n/a	n/a
8	POLR2A	chr6:26276939-26278086	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62653041..62655006-chr6:26277189..26278942,2	MCF-7	breast:
2	chr6:26275391..26278113-chr6:27778905..27781292,2	MCF-7	breast:

Variant related genes	Relation type
HIST1H2APS4	TF binding region
ENSG00000135655	Chromatin interaction
ENSG00000198673	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1124999	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1125000	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12526215	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2142703	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2393592	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2393593	0.90[EUR][1000 genomes]
rs2893843	1.00[YRI][hapmap]
rs34916901	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35310879	0.81[EUR][1000 genomes]
rs3999544	0.90[EUR][1000 genomes]
rs4412192	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4412193	1.00[YRI][hapmap]
rs6916289	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6930616	1.00[YRI][hapmap]
rs6931391	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939589	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6940237	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7450556	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7746807	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7747133	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7748935	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7761298	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769028	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7771202	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357004	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs9358915	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9358919	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9358927	1.00[YRI][hapmap]
rs9366649	0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9366651	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9379838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379842	1.00[YRI][hapmap]
rs9379843	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393690	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393691	1.00[YRI][hapmap]
rs9393692	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9393694	1.00[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989134	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
8	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
9	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
10	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
11	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
12	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
13	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
14	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
15	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26273600-26282800	Weak transcription	Spleen	Spleen
2	chr6:26273600-26283400	Weak transcription	Pancreas	Pancrea
3	chr6:26274200-26283000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:26274400-26282800	Weak transcription	Lung	lung
5	chr6:26274400-26284000	Weak transcription	Esophagus	oesophagus
6	chr6:26274400-26284600	Weak transcription	Ovary	ovary
7	chr6:26274600-26283600	Weak transcription	Stomach Mucosa	stomach
8	chr6:26274600-26284200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:26274800-26279400	Weak transcription	HSMMtube	muscle
10	chr6:26274800-26279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:26274800-26280400	Weak transcription	Placenta	Placenta
12	chr6:26274800-26280600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:26274800-26280800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:26274800-26280800	Weak transcription	Right Ventricle	heart
15	chr6:26274800-26281000	Weak transcription	Aorta	Aorta
16	chr6:26274800-26282600	Weak transcription	Hela-S3	cervix
17	chr6:26274800-26282800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:26274800-26282800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:26274800-26283200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr6:26274800-26283400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:26274800-26283400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:26274800-26283800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:26274800-26283800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:26275000-26277800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:26275000-26278800	Weak transcription	Fetal Lung	lung
26	chr6:26275000-26280600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:26275000-26280800	Weak transcription	Primary B cells from cord blood	blood
28	chr6:26275000-26281400	Weak transcription	GM12878-XiMat	blood
29	chr6:26275000-26282800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:26275000-26282800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:26275000-26282800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:26275000-26283000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:26275000-26283200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:26275000-26284400	Weak transcription	NHEK	skin
35	chr6:26275200-26280800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:26275200-26280800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:26275200-26282400	Weak transcription	Primary T cells from cord blood	blood
38	chr6:26275200-26283000	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:26275200-26283200	Weak transcription	Fetal Stomach	stomach
40	chr6:26275200-26283800	Weak transcription	Fetal Intestine Large	intestine
41	chr6:26275400-26278000	Enhancers	Dnd41	blood
42	chr6:26275400-26283000	Weak transcription	Fetal Intestine Small	intestine
43	chr6:26275400-26283400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:26275600-26283600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:26275800-26280600	Weak transcription	Thymus	Thymus
46	chr6:26275800-26284200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:26276000-26282800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:26276000-26283200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:26276000-26283600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:26276200-26281000	Weak transcription	Stomach Smooth Muscle	stomach

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