Variant report

Variant	rs3818947
Chromosome Location	chr6:26227104-26227105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:234744354..234747060-chr6:26225401..26227759,2	MCF-7	breast:
2	chr15:66160251..66163172-chr6:26224292..26227267,2	MCF-7	breast:
3	chr6:26055872..26058402-chr6:26225774..26227439,2	MCF-7	breast:
4	chr6:26030891..26034608-chr6:26223354..26228378,6	MCF-7	breast:
5	chr20:52966595..52969425-chr6:26225517..26227615,2	MCF-7	breast:
6	chr6:26226182..26228582-chr6:27775261..27778223,2	MCF-7	breast:
7	chr6:26225279..26227416-chr6:27859804..27863883,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203813	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000103769	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000168264	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000185130	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1000308	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]
rs10484437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341758	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16891404	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16891417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16891421	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891427	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891440	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891450	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891453	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[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];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891471	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891477	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16891497	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]
rs16891501	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]
rs16891505	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17533076	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17598764	0.87[EUR][1000 genomes]
rs17598927	1.00[ASW][hapmap]
rs17600910	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs34550794	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41266803	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41266805	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4593350	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55856153	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56360223	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56372675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61910695	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6913828	0.89[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	nsv883490	chr6:26172219-26231608	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	316 gene(s)	inside rSNPs	diseases
17	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3818947	HIST1H2BG	cis	multi-tissue	Pritchard
rs3818947	HIST1H2AE	cis	lymphoblastoid	seeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26223200-26227400	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:26223400-26227200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:26223400-26227400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:26223400-26227400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:26223400-26227400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:26223400-26227600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:26225400-26232400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:26225400-26232400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:26225400-26232600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:26225600-26227200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:26225600-26233400	Weak transcription	Colonic Mucosa	Colon
12	chr6:26225800-26227200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:26225800-26227400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:26225800-26229800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:26225800-26232400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:26225800-26232600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:26225800-26232600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:26225800-26233000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:26225800-26233000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:26225800-26233400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:26226000-26227200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:26226000-26227600	Enhancers	NHEK	skin
23	chr6:26226000-26230400	Weak transcription	Thymus	Thymus
24	chr6:26226000-26230400	Weak transcription	Osteobl	bone
25	chr6:26226000-26231200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:26226000-26233000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:26226000-26233200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:26226200-26232200	Weak transcription	A549	lung
29	chr6:26226200-26232400	Weak transcription	Primary T cells from cord blood	blood
30	chr6:26226200-26232400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:26226400-26227200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:26226400-26227200	Weak transcription	Spleen	Spleen
33	chr6:26226400-26227200	Weak transcription	GM12878-XiMat	blood
34	chr6:26226400-26227400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:26226400-26229000	Weak transcription	HepG2	liver
36	chr6:26226400-26229200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:26226400-26232600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:26226400-26232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:26226400-26232800	Weak transcription	Fetal Intestine Large	intestine
40	chr6:26226400-26233000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:26226400-26233000	Weak transcription	Placenta	Placenta
42	chr6:26226400-26233000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:26226400-26233000	Weak transcription	HMEC	breast
44	chr6:26226400-26233200	Weak transcription	Liver	Liver
45	chr6:26226400-26233200	Weak transcription	HUVEC	blood vessel
46	chr6:26226400-26233800	Weak transcription	Gastric	stomach
47	chr6:26226400-26234000	Weak transcription	HSMMtube	muscle
48	chr6:26226600-26227200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:26226600-26227200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:26226600-26227200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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