Variant report

Variant	rs198848
Chromosome Location	chr6:26106325-26106326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26105781..26107320-chr6:27094298..27096352,2	K562	blood:
2	chr2:178127973..178129753-chr6:26104564..26106585,2	K562	blood:
3	chr6:26052762..26068184-chr6:26093226..26113078,68	MCF-7	breast:
4	chr6:26104457..26106575-chr6:27858470..27861351,2	K562	blood:
5	chr6:26105568..26108288-chr6:27099915..27102205,2	K562	blood:
6	chr17:56734937..56737923-chr6:26104227..26106569,2	MCF-7	breast:
7	chr6:20207945..20211455-chr6:26105249..26107952,3	MCF-7	breast:
8	chr6:26104959..26107344-chr6:27777479..27779094,2	MCF-7	breast:
9	chr6:26105269..26107093-chr6:27796301..27798818,2	MCF-7	breast:
10	chr6:26019620..26034082-chr6:26100355..26110400,33	MCF-7	breast:
11	chr6:26045376..26048284-chr6:26104171..26106664,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIST1H4C-1	chr6:26105694-26107811	l_3139_chr6:26100862-26107811_brain

No data

Variant related genes	Relation type
ENSG00000124529	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000222043	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000116044	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000196532	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10425	0.91[CHD][hapmap];0.88[GIH][hapmap]
rs1068554	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs115810	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12346	0.91[CHD][hapmap];0.98[GIH][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs129129	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs1540275	0.86[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs1540276	0.86[CHB][hapmap]
rs169219	0.83[CHD][hapmap]
rs198801	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs198810	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198818	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198820	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198834	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198845	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs198847	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs198849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198852	0.88[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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198853	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs199737	0.86[CHB][hapmap]
rs199739	0.86[CHB][hapmap]
rs199741	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs199750	0.96[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap]
rs199751	0.86[CHB][hapmap]
rs199752	0.96[CHD][hapmap];0.90[MEX][hapmap]
rs199753	0.86[CHB][hapmap]
rs199754	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs2032447	0.87[CHD][hapmap];0.84[GIH][hapmap]
rs2213284	0.96[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs2230655	0.86[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs4401650	0.91[CHD][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap]
rs442601	0.86[CHB][hapmap]
rs6901039	0.86[CHB][hapmap];0.96[CHD][hapmap]
rs6922788	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs7756117	0.91[CHD][hapmap];0.84[GIH][hapmap]
rs807212	0.86[CHB][hapmap]
rs807214	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
8	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs198848	HIST1H1T	cis	multi-tissue	Pritchard
rs198848	HIST1H2BM	cis	cerebellum	SCAN
rs198848	HIST1H4I	cis	cerebellum	SCAN
rs198848	HIST1H2BB	cis	parietal	SCAN
rs198848	HIST1H2BD	cis	multi-tissue	Pritchard
rs198848	HIST1H2BC	cis	cerebellum	SCAN
rs198848	BTN2A2	cis	lymphoblastoid	seeQTL
rs198848	HIST1H2AA	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26104800-26106400	Enhancers	NHEK	skin
2	chr6:26104800-26117600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:26104800-26118800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:26104800-26122600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:26105000-26107000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:26105000-26107400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:26105000-26122600	Weak transcription	Right Atrium	heart
8	chr6:26105200-26107000	Weak transcription	Thymus	Thymus
9	chr6:26105600-26107200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:26105600-26107200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:26105800-26107200	Weak transcription	K562	blood
12	chr6:26105800-26109200	Weak transcription	Placenta	Placenta
13	chr6:26106200-26110200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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