Variant report

Variant	rs9368502
Chromosome Location	chr6:27300841-27300842
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:0)
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	chr6:27218055..27220276-chr6:27300325..27303096,3	K562	blood:
2	chr6:27298779..27303006-chr6:27440534..27442735,4	K562	blood:
3	chr6:27273015..27275740-chr6:27298464..27301159,2	K562	blood:
4	chr6:27299766..27302375-chr6:27444830..27446395,2	K562	blood:
5	chr6:27298898..27303175-chr6:27340830..27343404,5	K562	blood:
6	chr6:27287824..27293332-chr6:27295713..27302247,8	K562	blood:
7	chr6:27291413..27293040-chr6:27299829..27302713,2	MCF-7	breast:
8	chr6:27264150..27266831-chr6:27300629..27302449,2	K562	blood:
9	chr6:27300837..27303680-chr6:27307517..27309958,2	K562	blood:
10	chr6:27277495..27280431-chr6:27299498..27302391,2	K562	blood:
11	chr6:27263999..27267440-chr6:27299677..27302604,5	K562	blood:
12	chr6:27276791..27280576-chr6:27298923..27302888,5	K562	blood:
13	chr6:27299407..27301409-chr6:27341654..27343404,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction
ENSG00000220758	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000158553	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1127574	0.82[EUR][1000 genomes]
rs12199213	0.82[EUR][1000 genomes]
rs12213055	0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs17739727	0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs721600	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348761	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];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348762	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9379976	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9379977	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9379978	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393805	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393806	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393807	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9393808	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461362	0.86[ASW][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9468047	0.82[YRI][hapmap]
rs9468068	1.00[YRI][hapmap]
rs9468069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468076	0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883507	chr6:27279982-27318836	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2761047	chr6:27296775-27303927	Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9368502	ZNF391	cis	cerebellum	SCAN
rs9368502	ZNF204P	cis	cerebellum	SCAN
rs9368502	HIST1H4B	cis	parietal	SCAN
rs9368502	HIST1H2AL	cis	cerebellum	SCAN
rs9368502	BTN3A3	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27300200-27303200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27300200-27303400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:27300400-27301000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
4	chr6:27300400-27301600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:27300400-27301600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:27300400-27301600	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:27300400-27301800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:27300400-27301800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:27300400-27302000	Active TSS	GM12878-XiMat	blood
10	chr6:27300400-27302400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:27300400-27303200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:27300400-27303200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:27300400-27303400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:27300400-27303600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:27300600-27301000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr6:27300600-27301000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:27300600-27301000	Bivalent Enhancer	Fetal Heart	heart
18	chr6:27300600-27301000	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr6:27300600-27301000	Active TSS	Right Atrium	heart
20	chr6:27300600-27301000	Flanking Active TSS	HepG2	liver
21	chr6:27300600-27301200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
22	chr6:27300600-27301200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
23	chr6:27300600-27301200	Enhancers	Pancreas	Pancrea
24	chr6:27300600-27301200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr6:27300600-27301400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:27300600-27301400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:27300600-27301400	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:27300600-27301400	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
29	chr6:27300600-27301400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:27300600-27301400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:27300600-27301400	Active TSS	Ovary	ovary
32	chr6:27300600-27301600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr6:27300600-27301600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:27300600-27301600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:27300600-27301600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:27300600-27301600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:27300600-27301600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:27300600-27301600	Active TSS	NHLF	lung
39	chr6:27300600-27301800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:27300600-27302000	Active TSS	K562	blood
41	chr6:27300600-27302200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:27300600-27302200	Active TSS	HMEC	breast
43	chr6:27300800-27301000	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr6:27300800-27301000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:27300800-27301000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:27300800-27301000	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
47	chr6:27300800-27301000	Active TSS	Brain Substantia Nigra	brain
48	chr6:27300800-27301000	Bivalent/Poised TSS	Fetal Brain Female	brain
49	chr6:27300800-27301000	Bivalent Enhancer	Fetal Intestine Large	intestine
50	chr6:27300800-27301000	Bivalent Enhancer	Left Ventricle	heart

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