Variant report

Variant	rs10484438
Chromosome Location	chr6:26308287-26308288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26305172..26308456-chr6:26309318..26312208,7	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1053860	0.83[JPT][hapmap];0.85[YRI][hapmap]
rs10946810	0.83[JPT][hapmap]
rs11751646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11752014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11752120	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11752202	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11753590	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11754384	0.85[CEU][hapmap]
rs11754701	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11755795	0.83[CEU][hapmap]
rs11755996	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11756569	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11758318	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759682	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs11759720	0.82[CHB][hapmap]
rs12665035	0.82[JPT][hapmap]
rs16891520	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891523	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16891525	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[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16891529	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1883213	0.83[JPT][hapmap]
rs1883214	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393594	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2893820	0.83[JPT][hapmap]
rs2893842	0.91[JPT][hapmap]
rs2893843	0.81[JPT][hapmap]
rs34581160	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35190365	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35709300	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3734533	0.82[CHB][hapmap]
rs3778279	0.83[JPT][hapmap];0.82[YRI][hapmap]
rs3823157	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs4365922	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412193	0.81[JPT][hapmap]
rs4631273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59315883	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6899837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901243	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs6914596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6916643	0.91[CEU][hapmap]
rs6930616	0.81[JPT][hapmap]
rs6932584	0.89[JPT][hapmap]
rs73397342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73399344	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73399348	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73399351	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73399373	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73399386	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7755741	0.91[JPT][hapmap]
rs9358914	0.90[JPT][hapmap]
rs9358925	0.83[JPT][hapmap]
rs9358927	0.81[JPT][hapmap]
rs9366648	0.83[JPT][hapmap]
rs994379	0.83[JPT][hapmap];0.82[YRI][hapmap]

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	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	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
8	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
9	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
10	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10484438	ZNF193	cis	cerebellum	SCAN
rs10484438	ZNF165	cis	parietal	SCAN
rs10484438	HIST1H3E	cis	cerebellum	SCAN
rs10484438	HIST1H4F	cis	parietal	SCAN
rs10484438	HIST1H3E	cis	parietal	SCAN
rs10484438	ZKSCAN4	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26305600-26310200	Weak transcription	Psoas Muscle	Psoas
2	chr6:26305600-26311400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:26305600-26313400	Weak transcription	Small Intestine	intestine
4	chr6:26305800-26308800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:26305800-26309600	Weak transcription	Osteobl	bone
6	chr6:26305800-26309800	Weak transcription	HSMM	muscle
7	chr6:26305800-26310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:26305800-26310200	Weak transcription	Fetal Intestine Small	intestine
9	chr6:26305800-26310600	Weak transcription	Liver	Liver
10	chr6:26305800-26311000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:26305800-26311600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:26305800-26312000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:26305800-26312400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:26306000-26309800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:26306000-26309800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:26306000-26310000	Weak transcription	Fetal Kidney	kidney
17	chr6:26306000-26310000	Weak transcription	NHLF	lung
18	chr6:26306000-26310400	Enhancers	HepG2	liver
19	chr6:26306000-26311000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:26306200-26309600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:26306200-26309600	Weak transcription	Fetal Intestine Large	intestine
22	chr6:26306200-26309800	Weak transcription	NH-A	brain
23	chr6:26306200-26310000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:26306200-26310600	Weak transcription	Brain Angular Gyrus	brain
25	chr6:26306200-26310600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:26306200-26310800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:26306200-26311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:26306200-26311000	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:26306200-26311200	Weak transcription	Fetal Stomach	stomach
30	chr6:26306200-26311200	Enhancers	HMEC	breast
31	chr6:26306200-26311600	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:26306200-26311600	Weak transcription	Placenta	Placenta
33	chr6:26306200-26311600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:26306200-26311800	Weak transcription	Fetal Lung	lung
35	chr6:26306200-26312000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:26306400-26309800	Weak transcription	A549	lung
37	chr6:26306400-26310400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr6:26306400-26310600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:26306400-26311000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:26306400-26311200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr6:26306400-26311600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:26306400-26311600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:26306400-26312000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:26306600-26309800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:26306800-26309600	Enhancers	K562	blood
46	chr6:26306800-26310000	Weak transcription	NHDF-Ad	bronchial
47	chr6:26306800-26310600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:26306800-26310800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:26306800-26311800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr6:26307000-26308600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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