Variant report

Variant	rs16893937
Chromosome Location	chr6:28272868-28272869
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28270788..28272885-chr6:28303466..28306771,3	K562	blood:
2	chr6:28264442..28268560-chr6:28269964..28273646,5	K562	blood:
3	chr6:28217084..28219662-chr6:28271676..28274035,2	K562	blood:
4	chr6:28268157..28273166-chr6:28302896..28306229,5	K562	blood:
5	chr6:28271797..28274288-chr6:28283530..28286148,2	K562	blood:
6	chr6:28271633..28273346-chr6:28303958..28306016,2	MCF-7	breast:
7	chr6:28246460..28249146-chr6:28271252..28274232,2	K562	blood:
8	chr6:28271589..28273882-chr6:28298871..28300680,2	K562	blood:
9	chr6:28261083..28263249-chr6:28270818..28273469,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1062169	0.89[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1150697	0.80[CEU][hapmap]
rs1150699	0.80[CEU][hapmap]
rs1150704	0.80[CEU][hapmap]
rs1150713	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1150714	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11751702	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11752073	0.89[CEU][hapmap]
rs11756111	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11757730	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758148	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11758337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970439	1.00[JPT][hapmap]
rs1233664	0.80[CEU][hapmap]
rs1233665	0.80[CEU][hapmap]
rs1233666	0.80[CEU][hapmap]
rs1474589	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs16893817	0.80[CEU][hapmap]
rs16901846	1.00[CEU][hapmap];0.81[MKK][hapmap]
rs17301128	1.00[JPT][hapmap]
rs1736890	0.80[CEU][hapmap]
rs17776284	1.00[JPT][hapmap]
rs1778477	0.83[GIH][hapmap]
rs1890809	0.89[CEU][hapmap]
rs2185955	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2232422	1.00[CEU][hapmap]
rs2232428	0.89[CEU][hapmap]
rs2235358	1.00[JPT][hapmap]
rs2235359	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2281043	1.00[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes]
rs2299031	1.00[JPT][hapmap]
rs2622315	0.89[CEU][hapmap]
rs3800325	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3800326	1.00[JPT][hapmap]
rs55831267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56053755	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6456811	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6903652	1.00[JPT][hapmap]
rs6903823	0.88[JPT][hapmap]
rs6905368	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912584	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs6917759	0.89[CEU][hapmap]
rs6921919	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6922111	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6923170	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6929559	0.89[CEU][hapmap]
rs73740587	0.80[AMR][1000 genomes]
rs73742542	0.97[EUR][1000 genomes]
rs7741443	0.90[ASN][1000 genomes]
rs7744788	1.00[CEU][hapmap]
rs7769054	0.80[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs993619	0.80[CEU][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16893937	ZSCAN23	cis	parietal	SCAN
rs16893937	HMGN4	cis	parietal	SCAN
rs16893937	HIST1H4C	cis	parietal	SCAN
rs16893937	ZNF323	cis	parietal	SCAN
rs16893937	ZSCAN23	cis	cerebellum	SCAN
rs16893937	ZNF165	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:28250000-28293800	Weak transcription	Gastric	stomach
3	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
4	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
11	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
12	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
14	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:28255400-28278400	Weak transcription	HepG2	liver
16	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:28257600-28278800	Weak transcription	NHDF-Ad	bronchial
19	chr6:28257800-28279000	Weak transcription	HMEC	breast
20	chr6:28258400-28273800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:28258600-28273000	Weak transcription	Fetal Brain Male	brain
22	chr6:28264200-28273000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:28264200-28273000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:28264800-28274200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:28264800-28278600	Weak transcription	Fetal Intestine Small	intestine
26	chr6:28265000-28280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:28265400-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:28265600-28274000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:28266400-28278800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:28266800-28273400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:28268400-28280600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:28268800-28274400	Weak transcription	Fetal Stomach	stomach
33	chr6:28268800-28293400	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:28269000-28274200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:28269200-28275000	Weak transcription	Lung	lung
36	chr6:28269200-28278600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:28269200-28291600	Weak transcription	Right Ventricle	heart
38	chr6:28269400-28273400	Weak transcription	Fetal Thymus	thymus
39	chr6:28269400-28275200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:28269400-28278600	Weak transcription	Fetal Intestine Large	intestine
41	chr6:28269400-28280800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr6:28269600-28277400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:28269800-28273600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:28269800-28274400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:28269800-28277400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:28269800-28280000	Weak transcription	Left Ventricle	heart
47	chr6:28270000-28273600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:28270000-28273800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:28270000-28274000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:28270000-28275600	Weak transcription	Adipose Nuclei	Adipose

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