Variant report

Variant	rs1150704
Chromosome Location	chr6:28184371-28184372
allele	A/C
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28184339..28187958-chr6:28190844..28194750,7	MCF-7	breast:
2	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
3	chr6:28108272..28111912-chr6:28184259..28187979,3	MCF-7	breast:
4	chr6:27774472..27777190-chr6:28183511..28185747,2	K562	blood:
5	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
6	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:
7	chr6:28120467..28123016-chr6:28183065..28185019,2	MCF-7	breast:
8	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
9	chr6:28183176..28185636-chr6:28218176..28220356,3	MCF-7	breast:
10	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:

No data

Variant related genes	Relation type
ENSG00000217862	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10484404	0.90[CEU][hapmap]
rs1062169	0.94[GIH][hapmap];0.83[TSI][hapmap]
rs1150697	0.81[CEU][hapmap]
rs1150698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150714	0.80[CEU][hapmap]
rs11752073	0.90[CEU][hapmap]
rs11758148	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1233664	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233665	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474589	0.80[CEU][hapmap]
rs16893817	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16893937	0.80[CEU][hapmap]
rs16901846	0.80[CEU][hapmap]
rs1736890	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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736893	0.83[CHB][hapmap]
rs1736894	1.00[ASW][hapmap];0.91[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778469	0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778477	0.91[GIH][hapmap]
rs1890809	0.90[CEU][hapmap]
rs2232422	0.80[CEU][hapmap]
rs2281043	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs2622315	0.90[CEU][hapmap]
rs3800325	0.80[CEU][hapmap]
rs6456811	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs6917759	0.90[CEU][hapmap]
rs6923170	0.80[CEU][hapmap]
rs6929559	0.90[CEU][hapmap]
rs73740584	0.96[EUR][1000 genomes]
rs73740587	0.90[EUR][1000 genomes]
rs7744788	0.80[CEU][hapmap]
rs7769054	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs993619	1.00[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883514	chr6:28155418-28185726	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv883516	chr6:28156476-28185726	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1150704	ZSCAN23	cis	cerebellum	SCAN
rs1150704	ZNF192P1	cis	Adipose Subcutaneous	GTEx
rs1150704	ZNF323	cis	parietal	SCAN
rs1150704	HIST1H4C	cis	parietal	SCAN
rs1150704	HFE	cis	cerebellum	SCAN
rs1150704	AL022393.7	cis	Thyroid	GTEx
rs1150704	ZSCAN23	cis	parietal	SCAN
rs1150704	PARD6B	trans	cerebellum	SCAN
rs1150704	ZNF165	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28180800-28186400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:28181000-28185400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:28181400-28186000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:28181400-28186000	Weak transcription	HSMM	muscle
5	chr6:28181600-28185600	Weak transcription	GM12878-XiMat	blood
6	chr6:28182800-28186000	Enhancers	Placenta	Placenta
7	chr6:28183400-28184800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
8	chr6:28183600-28185600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:28183600-28186000	Weak transcription	HMEC	breast
10	chr6:28183600-28186200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:28183800-28185800	Enhancers	HepG2	liver
12	chr6:28184000-28184800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:28184000-28185000	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr6:28184000-28185800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:28184000-28186000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:28184000-28186000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:28184200-28184400	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr6:28184200-28184600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:28184200-28184600	Enhancers	Hela-S3	cervix
20	chr6:28184200-28185400	Enhancers	K562	blood
21	chr6:28184200-28185800	Weak transcription	Rectal Mucosa Donor 31	rectum

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