Variant report

Variant	rs1339899
Chromosome Location	chr6:28271602-28271603
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: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	chr6:28270484..28272247-chr6:28307860..28310847,2	K562	blood:
2	chr6:28270788..28272885-chr6:28303466..28306771,3	K562	blood:
3	chr6:28264442..28268560-chr6:28269964..28273646,5	K562	blood:
4	chr6:28270747..28272712-chr6:28309347..28312254,2	K562	blood:
5	chr6:28264329..28266427-chr6:28269486..28272144,3	K562	blood:
6	chr6:28268157..28273166-chr6:28302896..28306229,5	K562	blood:
7	chr6:28266856..28268560-chr6:28269964..28272119,2	K562	blood:
8	chr6:28246460..28249146-chr6:28271252..28274232,2	K562	blood:
9	chr6:28271589..28273882-chr6:28298871..28300680,2	K562	blood:
10	chr6:28261083..28263249-chr6:28270818..28273469,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10456362	0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1076639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11755032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11965538	0.82[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13200462	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1419183	0.82[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1679709	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1679732	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16894011	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1778507	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs1778508	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1778511	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17856167	1.00[CEU][hapmap]
rs1936365	0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs213239	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs213241	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs213243	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs213244	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2743554	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2743555	0.87[ASN][1000 genomes]
rs2799077	0.82[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2799079	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs61127718	0.82[ASN][1000 genomes]
rs68141011	0.88[ASN][1000 genomes]
rs6901575	0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6905391	0.87[ASN][1000 genomes]
rs6920512	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs73742521	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7740487	0.87[ASN][1000 genomes]
rs853676	0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs853678	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs853679	0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs853681	1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs853685	0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs853687	0.82[CEU][hapmap];0.90[CHB][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853688	0.82[ASN][1000 genomes]
rs853694	0.87[ASN][1000 genomes]
rs9295765	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9295766	0.81[ASN][1000 genomes]
rs9295767	0.81[ASN][1000 genomes]
rs9366717	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9380069	0.91[GIH][hapmap]
rs9393902	0.83[TSI][hapmap]
rs9393908	0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs9461446	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs9461448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9461449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9468322	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs9468325	0.81[ASN][1000 genomes]
rs9468342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9468345	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9986596	0.88[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1339899	ZSCAN31	cis	Thyroid	GTEx
rs1339899	ZSCAN31	cis	Nerve Tibial	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
2	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28250000-28293800	Weak transcription	Gastric	stomach
4	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
5	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
12	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
13	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
15	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:28255400-28278400	Weak transcription	HepG2	liver
17	chr6:28255600-28272000	Weak transcription	Brain Substantia Nigra	brain
18	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:28257600-28278800	Weak transcription	NHDF-Ad	bronchial
21	chr6:28257800-28279000	Weak transcription	HMEC	breast
22	chr6:28258400-28273800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:28258600-28273000	Weak transcription	Fetal Brain Male	brain
24	chr6:28264200-28273000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:28264200-28273000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:28264800-28272000	Weak transcription	HSMM	muscle
27	chr6:28264800-28274200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:28264800-28278600	Weak transcription	Fetal Intestine Small	intestine
29	chr6:28265000-28280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:28265400-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:28265600-28274000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:28266400-28278800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:28266800-28273400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:28268000-28272400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr6:28268400-28280600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:28268800-28274400	Weak transcription	Fetal Stomach	stomach
37	chr6:28268800-28293400	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:28269000-28274200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:28269200-28275000	Weak transcription	Lung	lung
40	chr6:28269200-28278600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:28269200-28291600	Weak transcription	Right Ventricle	heart
42	chr6:28269400-28273400	Weak transcription	Fetal Thymus	thymus
43	chr6:28269400-28275200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:28269400-28278600	Weak transcription	Fetal Intestine Large	intestine
45	chr6:28269400-28280800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:28269600-28277400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:28269800-28273600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:28269800-28274400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:28269800-28277400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:28269800-28280000	Weak transcription	Left Ventricle	heart

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