Variant report

Variant	rs6940237
Chromosome Location	chr6:26282322-26282323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26280810..26283122-chr6:27097500..27100402,2	MCF-7	breast:
2	chr17:57929104..57931344-chr6:26281644..26284303,2	MCF-7	breast:
3	chr6:26280162..26282434-chr6:27096276..27098558,2	MCF-7	breast:
4	chr6:26282088..26283672-chr6:27778250..27780102,2	MCF-7	breast:
5	chr6:26280754..26288136-chr6:27109918..27116629,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1124999	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1125000	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12526215	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2142703	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2179152	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2393592	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2393593	0.88[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs34916901	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35310879	0.83[EUR][1000 genomes]
rs3999544	0.96[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs4145910	1.00[JPT][hapmap]
rs4412192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6456712	0.84[EUR][1000 genomes]
rs6916289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6923139	0.87[MKK][hapmap]
rs6931391	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939589	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7450556	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs766406	1.00[JPT][hapmap]
rs766407	1.00[JPT][hapmap]
rs7746807	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7747133	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7748935	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7761298	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7769028	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771202	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357004	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9358915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358917	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9358919	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9366649	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9366651	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9379838	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9379843	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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393692	0.96[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9393693	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467703	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs9467704	0.93[YRI][hapmap]
rs989134	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6940237	ACOT13	cis	cerebellum	SCAN
rs6940237	HIST1H2BK	cis	parietal	SCAN
rs6940237	HIST1H4F	cis	parietal	SCAN
rs6940237	HIST1H3H	cis	parietal	SCAN
rs6940237	HIST1H3I	cis	parietal	SCAN

Chromatin state (count:74 , 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	chr6:26274800-26282600	Weak transcription	Hela-S3	cervix
10	chr6:26274800-26282800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:26274800-26282800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:26274800-26283200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:26274800-26283400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:26274800-26283400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:26274800-26283800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:26274800-26283800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:26275000-26282800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:26275000-26282800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr6:26275000-26282800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:26275000-26283000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:26275000-26283200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:26275000-26284400	Weak transcription	NHEK	skin
23	chr6:26275200-26282400	Weak transcription	Primary T cells from cord blood	blood
24	chr6:26275200-26283000	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:26275200-26283200	Weak transcription	Fetal Stomach	stomach
26	chr6:26275200-26283800	Weak transcription	Fetal Intestine Large	intestine
27	chr6:26275400-26283000	Weak transcription	Fetal Intestine Small	intestine
28	chr6:26275400-26283400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:26275600-26283600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:26275800-26284200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:26276000-26282800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:26276000-26283200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:26276000-26283600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:26276200-26284000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:26276200-26284000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:26276400-26283400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:26276600-26283400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:26276600-26283800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:26276800-26283400	Weak transcription	Colon Smooth Muscle	Colon
40	chr6:26277200-26283400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:26277400-26284200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:26277600-26282800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:26277600-26284200	Weak transcription	Brain Anterior Caudate	brain
44	chr6:26277800-26282600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:26277800-26284000	Weak transcription	Liver	Liver
46	chr6:26278600-26284200	Weak transcription	Brain Angular Gyrus	brain
47	chr6:26279600-26283400	Weak transcription	Fetal Lung	lung
48	chr6:26279800-26283600	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:26280600-26282400	Genic enhancers	Fetal Thymus	thymus
50	chr6:26281000-26284200	Enhancers	Dnd41	blood

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