Variant report

Variant	rs1000308
Chromosome Location	chr6:26244580-26244581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26244290..26246162-chr6:28911074..28913563,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204709	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10484437	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1341758	0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs16891404	0.87[ASN][1000 genomes]
rs16891417	0.89[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs16891421	0.97[ASN][1000 genomes]
rs16891427	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16891440	0.97[ASN][1000 genomes]
rs16891450	0.97[ASN][1000 genomes]
rs16891453	0.97[ASN][1000 genomes]
rs16891458	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs16891471	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16891477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891497	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891517	0.85[YRI][hapmap]
rs16891518	0.85[YRI][hapmap]
rs16891549	0.85[YRI][hapmap]
rs17533076	0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs17600910	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1883212	0.85[YRI][hapmap]
rs34550794	0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs3818947	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs41266803	0.87[ASN][1000 genomes]
rs41266805	0.87[ASN][1000 genomes]
rs41266827	0.83[AFR][1000 genomes]
rs4593350	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs55856153	0.97[ASN][1000 genomes]
rs56360223	0.97[ASN][1000 genomes]
rs56372675	0.97[ASN][1000 genomes]
rs61910695	0.90[ASN][1000 genomes]
rs6913828	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7450543	0.85[YRI][hapmap]
rs989710	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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
17	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1000308	HIST1H2AE	cis	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26241000-26250000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26241600-26246800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:26241800-26244600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr6:26241800-26245200	Enhancers	Fetal Intestine Small	intestine
5	chr6:26241800-26245600	Enhancers	Fetal Thymus	thymus
6	chr6:26241800-26246800	Enhancers	Fetal Intestine Large	intestine
7	chr6:26241800-26248000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:26241800-26249000	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:26241800-26249200	Weak transcription	Spleen	Spleen
10	chr6:26242000-26245400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:26242000-26245600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr6:26242000-26246800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:26242200-26249000	Weak transcription	Placenta	Placenta
14	chr6:26242400-26244800	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr6:26243000-26244600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:26243400-26245000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:26243800-26249400	Weak transcription	Hela-S3	cervix
18	chr6:26244000-26245000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr6:26244200-26244800	Weak transcription	Dnd41	blood
20	chr6:26244200-26245000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:26244200-26245200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr6:26244200-26247800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:26244200-26248200	Weak transcription	K562	blood
24	chr6:26244200-26248800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:26244200-26249600	Weak transcription	NHEK	skin
26	chr6:26244200-26249800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:26244400-26244800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:26244400-26244800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr6:26244400-26245200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:26244400-26247800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:26244400-26248400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:26244400-26248600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:26244400-26249400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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