Variant report

Variant	rs10946808
Chromosome Location	chr6:26233387-26233388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26233018..26235518-chr6:27781228..27784528,3	MCF-7	breast:
2	chr6:26025967..26028344-chr6:26231112..26233437,2	MCF-7	breast:
3	chr21:44526126..44528705-chr6:26232568..26234835,2	MCF-7	breast:
4	chr6:26232392..26235722-chr6:27100798..27102386,3	K562	blood:
5	chr19:1650911..1652489-chr6:26231971..26233838,2	K562	blood:
6	chr6:26231234..26236589-chr6:27099738..27104932,8	K562	blood:
7	chr3:183966623..183968865-chr6:26231934..26234192,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214160	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000160201	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000145194	Chromatin interaction
ENSG00000071564	Chromatin interaction
ENSG00000124529	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10946810	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11755492	1.00[YRI][hapmap]
rs11755943	0.82[JPT][hapmap]
rs11759720	0.82[JPT][hapmap]
rs12665035	1.00[YRI][hapmap]
rs17531978	1.00[YRI][hapmap]
rs17596719	1.00[YRI][hapmap]
rs1997768	0.82[JPT][hapmap]
rs2072802	1.00[YRI][hapmap]
rs2073526	1.00[YRI][hapmap]
rs2893842	1.00[YRI][hapmap]
rs35214279	0.81[EUR][1000 genomes]
rs3734533	0.82[JPT][hapmap]
rs4141885	1.00[YRI][hapmap]
rs7755741	0.89[MKK][hapmap];1.00[YRI][hapmap]
rs7766641	0.81[EUR][1000 genomes]
rs806794	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs811041	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358908	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9358912	0.82[EUR][1000 genomes]
rs9358913	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9358914	1.00[YRI][hapmap]
rs9358918	0.91[JPT][hapmap]
rs9358926	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs9379833	0.81[EUR][1000 genomes]
rs9379842	0.82[JPT][hapmap]
rs9393691	0.82[JPT][hapmap]

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

Variant related diseases (count:3)

Disease	PMID	Source
Height	18391951	GWAS catalog
Height	18391950	GWAS catalog
Height	19343178	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10946808	HIST1H2BF	cis	parietal	SCAN
rs10946808	ZNF193	cis	parietal	SCAN
rs10946808	HIST1H1C	cis	parietal	SCAN
rs10946808	ZSCAN23	cis	cerebellum	SCAN
rs10946808	BTN3A3	cis	lymphoblastoid	seeQTL
rs10946808	BTN3A2	cis	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26225600-26233400	Weak transcription	Colonic Mucosa	Colon
2	chr6:26225800-26233400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:26226400-26233800	Weak transcription	Gastric	stomach
4	chr6:26226400-26234000	Weak transcription	HSMMtube	muscle
5	chr6:26226600-26233600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:26227600-26233400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:26231200-26236000	Active TSS	Thymus	Thymus
8	chr6:26232000-26233400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:26232400-26236000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:26232600-26233400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:26232600-26233400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr6:26232600-26233800	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr6:26232600-26234200	Flanking Active TSS	Fetal Thymus	thymus
14	chr6:26232600-26234800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr6:26232600-26235800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:26232800-26233400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr6:26232800-26233400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:26232800-26233600	Flanking Active TSS	Fetal Intestine Small	intestine
19	chr6:26232800-26234000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:26232800-26234000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr6:26232800-26234000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr6:26232800-26234000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr6:26232800-26234000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr6:26232800-26234000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:26232800-26234200	Flanking Active TSS	GM12878-XiMat	blood
26	chr6:26232800-26234800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:26232800-26234800	Flanking Active TSS	K562	blood
28	chr6:26232800-26235000	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr6:26232800-26235000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:26232800-26235400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:26232800-26235600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr6:26232800-26235600	Active TSS	Aorta	Aorta
33	chr6:26232800-26235800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:26232800-26235800	Active TSS	Fetal Lung	lung
35	chr6:26233000-26233400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
36	chr6:26233000-26233400	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr6:26233000-26233400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:26233000-26233400	Active TSS	Brain Germinal Matrix	brain
39	chr6:26233000-26233400	Enhancers	Placenta Amnion	Placenta Amnion
40	chr6:26233000-26233600	Active TSS	Fetal Brain Female	brain
41	chr6:26233000-26233800	Enhancers	HMEC	breast
42	chr6:26233000-26233800	Active TSS	Osteobl	bone
43	chr6:26233000-26234000	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr6:26233000-26234000	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr6:26233000-26234200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr6:26233000-26234200	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr6:26233000-26234200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr6:26233000-26234400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr6:26233000-26235000	Flanking Active TSS	Dnd41	blood
50	chr6:26233000-26235400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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