Variant report

Variant	rs10484436
Chromosome Location	chr6:26237155-26237156
allele	C/T
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	chr6:26233034-26244857	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26236162..26238917-chr6:27099673..27101355,2	MCF-7	breast:
2	chr6:26237129..26239428-chr6:27101709..27103501,2	K562	blood:
3	chr3:28388905..28390597-chr6:26234908..26237633,2	K562	blood:

Variant related genes	Relation type
HIST1H4F	TF binding region
HIST1H1D	TF binding region
ENSG00000196787	Chromatin interaction
ENSG00000163512	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10452600	1.00[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11753131	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753625	0.86[EUR][1000 genomes]
rs11753655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754744	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11755210	0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11755943	0.90[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11757394	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11757754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758351	0.82[ASW][hapmap];0.93[CHD][hapmap];0.80[LWK][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11759720	0.85[CHD][hapmap]
rs11759904	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341759	1.00[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16891378	1.00[ASW][hapmap];0.93[CHD][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16891397	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16891401	0.89[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16891405	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16891443	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891446	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891455	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891456	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891466	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891467	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891474	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16891481	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17598927	0.89[CHB][hapmap];0.93[CHD][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs1997768	0.90[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2022448	0.88[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2050948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069018	0.90[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2069019	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2069020	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2143345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143346	1.00[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2143347	0.89[CHB][hapmap];0.93[CHD][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs2183948	0.85[EUR][1000 genomes]
rs3734530	0.88[CHB][hapmap]
rs3734533	0.93[CHD][hapmap];0.80[LWK][hapmap]
rs3757135	1.00[ASW][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41266801	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41266807	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55643278	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55815656	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55848726	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56186759	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56220351	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56398712	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
16	nsv1021294	chr6:26190316-26246784	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	309 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10484436	HIST1H3E	cis	cerebellum	SCAN
rs10484436	ZNF187	cis	parietal	SCAN
rs10484436	HIST1H3F	cis	cerebellum	SCAN
rs10484436	HIST1H1D	cis	cerebellum	SCAN
rs10484436	HIST1H4F	cis	parietal	SCAN
rs10484436	HIST1H2BF	cis	parietal	SCAN
rs10484436	HIST1H2BJ	cis	lymphoblastoid	seeQTL
rs10484436	HIST1H4F	cis	cerebellum	SCAN
rs10484436	TNFRSF1A	trans	parietal	SCAN
rs10484436	HIST1H2AE	cis	lymphoblastoid	seeQTL
rs10484436	HIST1H3E	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26235400-26240000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:26235400-26240000	Weak transcription	Placenta	Placenta
3	chr6:26235400-26240400	Weak transcription	Esophagus	oesophagus
4	chr6:26235800-26240000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:26235800-26240000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:26235800-26240000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:26235800-26240000	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:26235800-26240200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:26235800-26240200	Weak transcription	Fetal Brain Male	brain
10	chr6:26235800-26240200	Weak transcription	HMEC	breast
11	chr6:26235800-26240400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:26236000-26237400	Enhancers	Dnd41	blood
13	chr6:26236000-26237600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:26236000-26240000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:26236000-26240000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:26236000-26240200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:26236000-26240200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:26236000-26240200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:26236000-26240200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:26236000-26240200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:26236000-26240200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:26236000-26240200	Weak transcription	NHEK	skin
23	chr6:26236000-26240400	Weak transcription	Stomach Mucosa	stomach
24	chr6:26236000-26240600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:26236200-26239800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr6:26236200-26239800	Weak transcription	Fetal Thymus	thymus
27	chr6:26236200-26240000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:26236200-26240000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:26236200-26240000	Weak transcription	Fetal Intestine Large	intestine
30	chr6:26236200-26240000	Weak transcription	Fetal Intestine Small	intestine
31	chr6:26236200-26240200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:26236200-26240200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr6:26236200-26240200	Weak transcription	Primary B cells from cord blood	blood
34	chr6:26236200-26240200	Weak transcription	Primary T cells from cord blood	blood
35	chr6:26236200-26240200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:26236200-26240200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:26236200-26240200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:26236200-26240200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:26236200-26240200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:26236200-26240200	Weak transcription	Brain Germinal Matrix	brain
41	chr6:26236200-26240200	Weak transcription	HUVEC	blood vessel
42	chr6:26236200-26240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:26236400-26240200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:26236400-26240200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr6:26236400-26240200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:26236400-26240400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr6:26236600-26240200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:26236600-26240200	Weak transcription	GM12878-XiMat	blood
49	chr6:26236600-26240400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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