Variant report

Variant	rs1474589
Chromosome Location	chr6:28321544-28321545
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
2	chr6:28217257..28219975-chr6:28319678..28321725,2	K562	blood:
3	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
4	chr6:28108695..28111169-chr6:28321228..28323056,2	K562	blood:
5	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
6	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
7	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

Variant related genes	Relation type
ENSG00000197062	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000176933	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1016069	0.80[YRI][hapmap]
rs1062169	0.89[CEU][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs1150697	0.80[CEU][hapmap]
rs1150699	0.80[CEU][hapmap]
rs1150704	0.80[CEU][hapmap]
rs1150713	0.93[EUR][1000 genomes]
rs1150714	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11751702	0.80[EUR][1000 genomes]
rs11752073	0.89[CEU][hapmap]
rs11756111	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11757730	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11758148	1.00[JPT][hapmap]
rs11758337	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11970439	1.00[JPT][hapmap]
rs1233664	0.80[CEU][hapmap]
rs1233665	0.80[CEU][hapmap]
rs1233666	0.80[CEU][hapmap]
rs13190937	0.81[ASW][hapmap]
rs13215804	0.81[ASW][hapmap]
rs16893817	0.80[CEU][hapmap]
rs16893937	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs16894116	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs16901846	1.00[CEU][hapmap]
rs16901847	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs17301128	1.00[JPT][hapmap]
rs1736890	0.80[CEU][hapmap]
rs17776284	1.00[JPT][hapmap]
rs2185955	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2232422	1.00[CEU][hapmap]
rs2232428	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs2235358	1.00[JPT][hapmap]
rs2235359	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2281043	1.00[CEU][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs2299031	1.00[JPT][hapmap]
rs2622315	0.89[CEU][hapmap]
rs35875412	0.81[AFR][1000 genomes]
rs3800325	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3800326	1.00[JPT][hapmap]
rs55831267	0.97[EUR][1000 genomes]
rs56053755	0.91[EUR][1000 genomes]
rs56295386	0.92[AFR][1000 genomes]
rs6456811	1.00[CEU][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs6903652	1.00[JPT][hapmap]
rs6903823	0.88[JPT][hapmap]
rs6905368	0.97[EUR][1000 genomes]
rs6912584	0.89[GIH][hapmap];1.00[JPT][hapmap]
rs6917759	0.89[CEU][hapmap]
rs6921919	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6922111	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6923170	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6929559	0.89[CEU][hapmap]
rs71559082	0.87[AFR][1000 genomes]
rs73742542	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744788	1.00[CEU][hapmap]
rs7765989	0.85[AFR][1000 genomes]
rs7769054	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs993619	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1474589	ZSCAN23	cis	parietal	SCAN
rs1474589	HIST1H4C	cis	parietal	SCAN
rs1474589	PGBD1	cis	multi-tissue	Pritchard
rs1474589	ZSCAN23	cis	cerebellum	SCAN
rs1474589	ZNF165	cis	parietal	SCAN
rs1474589	ZNF323	cis	parietal	SCAN
rs1474589	HMGN4	cis	parietal	SCAN
rs1474589	PGBD1	cis	Liver	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28317200-28322000	Active TSS	Rectal Smooth Muscle	rectum
2	chr6:28317200-28322200	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:28318200-28321800	Weak transcription	Spleen	Spleen
4	chr6:28318200-28322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:28318400-28321600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:28318400-28321600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:28318400-28321800	Weak transcription	Gastric	stomach
8	chr6:28318400-28322200	Weak transcription	Placenta	Placenta
9	chr6:28318400-28323000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:28318400-28323600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:28318600-28322800	Weak transcription	NHDF-Ad	bronchial
14	chr6:28318600-28323000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:28318800-28322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:28318800-28322800	Weak transcription	Fetal Kidney	kidney
17	chr6:28319000-28321600	Weak transcription	Osteobl	bone
18	chr6:28319000-28323000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:28319000-28323200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:28319000-28323200	Weak transcription	Small Intestine	intestine
21	chr6:28319200-28321600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:28319200-28321600	Weak transcription	Fetal Stomach	stomach
23	chr6:28319200-28321800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:28319200-28322000	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr6:28319200-28322200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:28319200-28322200	Weak transcription	Lung	lung
27	chr6:28319200-28322200	Weak transcription	A549	lung
28	chr6:28319200-28322200	Weak transcription	HMEC	breast
29	chr6:28319200-28322400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:28319200-28322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:28319200-28322800	Weak transcription	Right Ventricle	heart
32	chr6:28319200-28323000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:28319200-28323000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:28319200-28323000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:28319200-28323000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:28319200-28323000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:28319200-28323000	Weak transcription	Fetal Intestine Large	intestine
38	chr6:28319200-28323200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:28319200-28323200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr6:28319200-28323200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:28319200-28323200	Weak transcription	Fetal Intestine Small	intestine
42	chr6:28319200-28323400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:28319200-28323400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:28319200-28323600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr6:28319200-28323600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:28319200-28323600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:28319400-28321800	Weak transcription	NHLF	lung
48	chr6:28319400-28322200	Weak transcription	Right Atrium	heart
49	chr6:28319400-28322200	Weak transcription	NH-A	brain
50	chr6:28319400-28322800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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