Variant report

Variant	rs6926126
Chromosome Location	chr6:25278546-25278547
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	KAP1	chr6:25278193-25279426	HEK293	kidney:	n/a	n/a
2	GATA2	chr6:25278361-25279446	SH-SY5Y	brain:	n/a	chr6:25278424-25278440 chr6:25278422-25278443 chr6:25278429-25278436 chr6:25278429-25278436 chr6:25278429-25278436 chr6:25278644-25278654
3	CTCF	chr6:25278481-25280742	SK-N-SH	brain:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
4	CHD2	chr6:25278538-25280897	Hela-S3	cervix:	n/a	chr6:25279278-25279288
5	ZNF263	chr6:25278178-25281125	HEK293-T-REx	kidney:	n/a	chr6:25280300-25280309 chr6:25278453-25278462
6	SMC3	chr6:25278534-25278693	GM12878	blood:	n/a	n/a
7	SMARCC1	chr6:25278460-25281460	Hela-S3	cervix:	n/a	n/a
8	SMC3	chr6:25277805-25281298	SK-N-SH	brain:	n/a	chr6:25279245-25279259
9	REST	chr6:25278540-25280544	H1-neurons	neurons:	n/a	chr6:25278554-25278574

No.	Distal block	Cell Line	Cell type
1	chr6:25277631..25279275-chr6:25301822..25304144,2	MCF-7	breast:
2	chr6:25277929..25281528-chr6:25281560..25287992,8	MCF-7	breast:
3	chr6:25277697..25280622-chr6:25286931..25288666,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213972	TF binding region
LRRC16A	TF binding region
ENSG00000207286	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1016854	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1016855	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018839	0.82[CHD][hapmap]
rs2050044	0.88[EUR][1000 genomes]
rs2064211	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2078527	0.88[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2690054	0.91[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2690064	0.86[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2690134	0.82[CHD][hapmap]
rs2744257	0.91[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.87[ASN][1000 genomes]
rs2744258	0.87[CEU][hapmap];0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs2744267	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2744269	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744288	0.82[CHD][hapmap]
rs2744294	0.82[CHD][hapmap]
rs6908902	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909014	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914799	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721036	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs721037	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs723047	0.91[EUR][1000 genomes]
rs723048	0.91[CEU][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7748256	0.87[EUR][1000 genomes]
rs9356971	0.87[EUR][1000 genomes]
rs9356972	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs9358848	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9358849	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs9366614	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs9379746	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs9379747	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs9379750	0.88[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs9393636	0.85[EUR][1000 genomes]
rs9393637	0.88[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6926126	HIST1H3B	cis	cerebellum	SCAN
rs6926126	HIST1H4L	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25275600-25278600	Weak transcription	Colonic Mucosa	Colon
2	chr6:25276200-25278600	Enhancers	Liver	Liver
3	chr6:25276200-25278600	Enhancers	Fetal Lung	lung
4	chr6:25277000-25278600	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:25277200-25278600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:25277200-25278600	Enhancers	Fetal Brain Male	brain
7	chr6:25277200-25278600	Enhancers	Fetal Intestine Large	intestine
8	chr6:25277400-25278600	Enhancers	Primary hematopoietic stem cells	blood
9	chr6:25277400-25278600	Enhancers	Adipose Nuclei	Adipose
10	chr6:25277400-25278600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:25277600-25278600	Weak transcription	Primary B cells from cord blood	blood
12	chr6:25277600-25278600	Weak transcription	Small Intestine	intestine
13	chr6:25277800-25278600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:25277800-25278600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:25278000-25278600	Enhancers	A549	lung
16	chr6:25278000-25278600	Enhancers	GM12878-XiMat	blood
17	chr6:25278000-25278600	Enhancers	NHDF-Ad	bronchial
18	chr6:25278000-25278800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:25278000-25279000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:25278200-25278600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:25278200-25278600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr6:25278200-25278600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:25278200-25278600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:25278200-25278600	Enhancers	Brain Anterior Caudate	brain
25	chr6:25278200-25278600	Bivalent Enhancer	Brain Hippocampus Middle	brain
26	chr6:25278200-25278600	Enhancers	Stomach Mucosa	stomach
27	chr6:25278200-25278600	Enhancers	Osteobl	bone
28	chr6:25278200-25278800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:25278200-25278800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr6:25278200-25278800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr6:25278200-25278800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr6:25278200-25278800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr6:25278200-25278800	Enhancers	Fetal Heart	heart
34	chr6:25278200-25278800	Enhancers	NH-A	brain
35	chr6:25278200-25279000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr6:25278200-25279000	Flanking Active TSS	Hela-S3	cervix
37	chr6:25278200-25279200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:25278400-25278600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr6:25278400-25278600	Enhancers	Primary T cells from cord blood	blood
40	chr6:25278400-25278600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr6:25278400-25278600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:25278400-25278600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr6:25278400-25278600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:25278400-25278600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:25278400-25278600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
46	chr6:25278400-25278600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:25278400-25278600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:25278400-25278600	Flanking Active TSS	Aorta	Aorta
49	chr6:25278400-25278600	Bivalent Enhancer	Brain Angular Gyrus	brain
50	chr6:25278400-25278600	Bivalent Enhancer	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links