Variant report

Variant	rs6930616
Chromosome Location	chr6:26331969-26331970
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:13)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:26329307..26333799-chr6:26568024..26573999,9	K562	blood:
2	chr6:26216015..26217608-chr6:26329315..26332026,2	MCF-7	breast:
3	chr6:26330749..26333675-chr6:26599169..26602051,2	K562	blood:
4	chr6:26327903..26334280-chr6:26553526..26557732,8	K562	blood:
5	chr6:26330167..26332009-chr6:26561007..26562531,2	K562	blood:
6	chr6:26331657..26333799-chr6:26567368..26569524,2	K562	blood:
7	chr6:26331324..26332922-chr6:27100115..27102380,2	K562	blood:
8	chr6:26329309..26333130-chr6:26553526..26558565,5	K562	blood:
9	chr6:26329107..26333235-chr6:26529334..26532709,3	K562	blood:
10	chr6:26328637..26334167-chr6:26519696..26523328,10	K562	blood:
11	chr6:26330362..26332555-chr6:26595064..26597595,2	MCF-7	breast:
12	chr6:26330591..26334286-chr6:26537283..26540361,5	K562	blood:
13	chr6:26328431..26333737-chr6:26535954..26540361,8	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BTN3A2-1	chr6:26331955-26332135	XLOC_005209
2	lnc-BTN3A2-1	chr6:26331953-26332135	XLOC_005209
3	lnc-HIST1H4H-3	chr6:26331955-26332365	NONHSAT108263
4	lnc-BTN3A2-1	chr6:26331952-26332353	NONHSAT108266

No data

Variant related genes	Relation type
ENSG00000146109	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000182952	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1053860	0.83[JPT][hapmap]
rs10946810	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs11751978	0.81[JPT][hapmap]
rs11752014	0.81[JPT][hapmap]
rs11755943	0.90[JPT][hapmap]
rs11759682	0.90[JPT][hapmap]
rs11759720	0.90[JPT][hapmap]
rs12525187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660432	0.82[EUR][1000 genomes]
rs12665035	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs16891523	0.81[JPT][hapmap]
rs16891525	0.81[JPT][hapmap]
rs17608582	0.82[EUR][1000 genomes]
rs1883213	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs1883214	0.81[JPT][hapmap]
rs1987244	0.81[EUR][1000 genomes]
rs1997768	0.90[JPT][hapmap]
rs2893820	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs2893842	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs2893843	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734533	0.90[JPT][hapmap]
rs3778279	0.83[JPT][hapmap]
rs3823157	0.90[JPT][hapmap]
rs4412193	1.00[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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4631273	0.81[JPT][hapmap]
rs61324092	0.81[EUR][1000 genomes]
rs62394764	0.81[EUR][1000 genomes]
rs62394768	0.82[EUR][1000 genomes]
rs6901243	0.90[JPT][hapmap]
rs6908402	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6914596	0.81[JPT][hapmap]
rs6917995	0.81[ASN][1000 genomes]
rs6918325	0.82[EUR][1000 genomes]
rs725575	0.81[EUR][1000 genomes]
rs7755741	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs9357005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9358914	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs9358916	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9358918	0.91[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9358920	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9358925	0.92[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs9358926	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs9358927	1.00[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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366648	0.88[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs9366650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9379844	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9379846	0.82[EUR][1000 genomes]
rs9393691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9393693	1.00[YRI][hapmap]
rs9393696	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9393697	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs994379	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv5230	chr6:26321593-26361531	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6930616	ACOT13	cis	cerebellum	SCAN
rs6930616	WDR90	trans	parietal	SCAN
rs6930616	HIST1H3C	cis	parietal	SCAN
rs6930616	HIST1H4H	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26326600-26332800	Active TSS	A549	lung
2	chr6:26327200-26333000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:26329600-26333200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:26330000-26333400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:26330200-26332000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:26330200-26332000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:26330200-26333200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:26330200-26333400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:26330400-26332200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:26330400-26332200	Active TSS	Hela-S3	cervix
11	chr6:26330400-26332600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:26330400-26332800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr6:26330400-26332800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:26330600-26332000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr6:26330600-26332000	Flanking Active TSS	HUVEC	blood vessel
16	chr6:26330600-26332200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:26330600-26332600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:26330600-26332600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:26330600-26332600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
20	chr6:26330600-26332600	Flanking Active TSS	Osteobl	bone
21	chr6:26330600-26332800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:26330600-26333000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:26330600-26333000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:26330600-26333000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr6:26330600-26333600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:26330800-26332000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:26330800-26332200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
28	chr6:26330800-26332400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
29	chr6:26330800-26332800	Bivalent/Poised TSS	HepG2	liver
30	chr6:26331000-26332000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
31	chr6:26331000-26332200	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr6:26331000-26332400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:26331000-26332400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
34	chr6:26331000-26332400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
35	chr6:26331000-26332400	Bivalent Enhancer	Fetal Stomach	stomach
36	chr6:26331000-26332600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:26331000-26332600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr6:26331000-26332600	Flanking Active TSS	K562	blood
39	chr6:26331000-26333000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:26331000-26333000	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr6:26331200-26332000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:26331200-26332200	Bivalent/Poised TSS	Psoas Muscle	Psoas
43	chr6:26331200-26332400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
44	chr6:26331200-26332600	Active TSS	HSMM	muscle
45	chr6:26331200-26333000	Bivalent Enhancer	Fetal Heart	heart
46	chr6:26331200-26333000	Active TSS	GM12878-XiMat	blood
47	chr6:26331400-26332000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:26331400-26332000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
49	chr6:26331400-26332200	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr6:26331400-26332400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links