Variant report

Variant	rs9379829
Chromosome Location	chr6:26172219-26172220
allele	C/T
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:0)
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	chr6:26171710..26174567-chr6:26566701..26569487,2	K562	blood:
2	chr6:26031547..26033237-chr6:26171719..26173813,2	MCF-7	breast:
3	chr6:26170156..26172522-chr6:26452443..26454404,2	K562	blood:
4	chr6:26170252..26172933-chr6:26517491..26519149,2	K562	blood:
5	chr17:59940856..59941821-chr6:26172204..26172843,2	HCT-116	colon:
6	chr6:26171577..26173697-chr6:27830155..27831800,2	MCF-7	breast:
7	chr6:26172143..26175522-chr6:26519763..26522796,4	K562	blood:
8	chr6:26170534..26173116-chr6:26582470..26585012,2	K562	blood:
9	chr12:4382880..4383483-chr6:26172077..26172594,2	NB4	blood:
10	chr19:49954728..49955367-chr6:26171993..26172793,2	Hela-S3	cervix:
11	chr6:26172209..26174275-chr6:27100538..27103106,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000118971	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000104872	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1009181	0.85[CHD][hapmap]
rs10484437	0.85[MKK][hapmap]
rs1341758	0.87[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs16891417	0.96[MKK][hapmap]
rs16891512	0.91[MKK][hapmap]
rs16891517	0.91[MKK][hapmap]
rs16891518	0.91[MKK][hapmap]
rs17533076	0.87[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs17600910	0.91[MKK][hapmap]
rs2066295	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2183947	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34550794	0.96[MKK][hapmap];1.00[YRI][hapmap]
rs4486004	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4593350	1.00[YRI][hapmap]
rs72834694	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72834696	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7450543	0.91[MKK][hapmap]
rs806973	0.85[CHD][hapmap]
rs9358909	0.83[ASN][1000 genomes]
rs9366639	0.82[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.99[ASN][1000 genomes]
rs9379827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379831	0.89[CHD][hapmap]
rs989710	0.96[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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
19	nsv518431	chr6:26148311-26211368	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases
20	nsv526456	chr6:26148311-26211368	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases
21	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9379829	ZSCAN23	cis	cerebellum	SCAN
rs9379829	HIST1H3H	cis	parietal	SCAN
rs9379829	HIST1H1C	cis	parietal	SCAN
rs9379829	HIST1H2BJ	cis	cerebellum	SCAN
rs9379829	TBC1D30	trans	lymphoblastoid	seeQTL
rs9379829	HIST1H4H	cis	parietal	SCAN
rs9379829	SCGN	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26170400-26174200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:26171200-26172800	Active TSS	Fetal Brain Male	brain
3	chr6:26171200-26173600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:26171200-26173600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:26171200-26173600	Active TSS	Thymus	Thymus
6	chr6:26171400-26173400	Active TSS	Primary T cells fromperipheralblood	blood
7	chr6:26171400-26173600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:26171400-26173600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:26171400-26173800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:26171400-26173800	Active TSS	Psoas Muscle	Psoas
11	chr6:26171400-26174000	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:26171400-26174000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:26171600-26173000	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr6:26171600-26173200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:26171600-26173200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:26171600-26173200	Active TSS	Brain Cingulate Gyrus	brain
17	chr6:26171600-26173200	Active TSS	Fetal Muscle Trunk	muscle
18	chr6:26171600-26173600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:26171600-26173600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:26171600-26173600	Active TSS	Aorta	Aorta
21	chr6:26171600-26173600	Active TSS	Right Ventricle	heart
22	chr6:26171600-26173600	Active TSS	HMEC	breast
23	chr6:26171600-26173800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:26171600-26173800	Active TSS	Colonic Mucosa	Colon
25	chr6:26171600-26173800	Active TSS	Fetal Stomach	stomach
26	chr6:26171600-26173800	Active TSS	Right Atrium	heart
27	chr6:26171600-26173800	Active TSS	A549	lung
28	chr6:26171600-26173800	Active TSS	NHLF	lung
29	chr6:26171600-26174000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr6:26171600-26174000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:26171800-26172600	Active TSS	Primary hematopoietic stem cells	blood
32	chr6:26171800-26172800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr6:26171800-26172800	Active TSS	Fetal Muscle Leg	muscle
34	chr6:26171800-26172800	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr6:26171800-26173000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:26171800-26173000	Active TSS	Small Intestine	intestine
37	chr6:26171800-26173200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:26171800-26173200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:26171800-26173200	Active TSS	Esophagus	oesophagus
40	chr6:26171800-26173200	Active TSS	Fetal Heart	heart
41	chr6:26171800-26173200	Active TSS	Lung	lung
42	chr6:26171800-26173200	Active TSS	Placenta Amnion	Placenta Amnion
43	chr6:26171800-26173400	Active TSS	Primary B cells from peripheral blood	blood
44	chr6:26171800-26173400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:26171800-26173400	Active TSS	Duodenum Mucosa	Duodenum
46	chr6:26171800-26173400	Active TSS	Pancreas	Pancrea
47	chr6:26171800-26173600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:26171800-26173600	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr6:26171800-26173600	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr6:26171800-26173600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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