Variant report

Variant	rs2743554
Chromosome Location	chr6:28265640-28265641
allele	C/T
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	chr6:28263544..28266110-chr6:28280477..28282083,2	K562	blood:
2	chr6:28264442..28268560-chr6:28269964..28273646,5	K562	blood:
3	chr6:28264981..28267059-chr6:28281908..28283935,2	MCF-7	breast:
4	chr6:28255681..28258623-chr6:28265550..28268633,3	K562	blood:
5	chr6:28252167..28254655-chr6:28264060..28265912,2	MCF-7	breast:
6	chr6:28264732..28267471-chr6:28301531..28305480,4	K562	blood:
7	chr6:28265276..28267226-chr6:28297300..28300691,3	MCF-7	breast:
8	chr6:28264329..28266427-chr6:28269486..28272144,3	K562	blood:
9	chr6:28265086..28267081-chr6:28267676..28269860,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10456362	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1076639	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11755032	0.82[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11965538	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13200462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1339899	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1419183	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1679709	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1679732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1778507	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1778508	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1778511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17856167	0.82[CEU][hapmap]
rs1936365	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs213239	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs213241	0.82[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs213243	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs213244	0.82[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2743555	0.97[ASN][1000 genomes]
rs2799077	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2799079	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[ASN][1000 genomes]
rs68141011	0.96[ASN][1000 genomes]
rs6901575	0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6905391	0.97[ASN][1000 genomes]
rs6920512	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs7740487	0.94[ASN][1000 genomes]
rs853676	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[ASN][1000 genomes]
rs853678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs853679	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs853681	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs853682	0.87[ASN][1000 genomes]
rs853685	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs853687	0.83[ASN][1000 genomes]
rs853688	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs853694	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9295765	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9366717	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs9380069	0.91[GIH][hapmap]
rs9393908	0.88[JPT][hapmap]
rs9461446	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9461448	0.82[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9461449	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9468321	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9468322	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9468342	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9468345	1.00[JPT][hapmap]
rs9986596	0.96[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
rs2743554	HIST1H4J	cis	lymphoblastoid	seeQTL
rs2743554	ZSCAN31	cis	Nerve Tibial	GTEx

Chromatin state (count:97 , 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	chr6:28250600-28267000	Weak transcription	NHEK	skin
7	chr6:28250600-28270800	Weak transcription	Fetal Heart	heart
8	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:28250800-28270000	Weak transcription	Psoas Muscle	Psoas
10	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:28251000-28270800	Weak transcription	Colonic Mucosa	Colon
12	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:28255200-28268600	Weak transcription	Ovary	ovary
16	chr6:28255200-28271200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:28255200-28271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
19	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
20	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
22	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:28255400-28271200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:28255400-28278400	Weak transcription	HepG2	liver
25	chr6:28255600-28271400	Weak transcription	Placenta	Placenta
26	chr6:28255600-28272000	Weak transcription	Brain Substantia Nigra	brain
27	chr6:28256000-28267600	Weak transcription	Osteobl	bone
28	chr6:28256400-28268400	Weak transcription	Fetal Intestine Large	intestine
29	chr6:28256400-28271600	Weak transcription	Liver	Liver
30	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:28256600-28268200	Weak transcription	Lung	lung
32	chr6:28256600-28268600	Weak transcription	Fetal Thymus	thymus
33	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:28257600-28268000	Weak transcription	K562	blood
35	chr6:28257600-28268400	Weak transcription	Right Ventricle	heart
36	chr6:28257600-28278800	Weak transcription	NHDF-Ad	bronchial
37	chr6:28257800-28268600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:28257800-28279000	Weak transcription	HMEC	breast
39	chr6:28258000-28268200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:28258000-28268600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:28258000-28268800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:28258000-28270800	Weak transcription	NH-A	brain
43	chr6:28258200-28268000	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:28258200-28268600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:28258400-28268400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:28258400-28269600	Weak transcription	Fetal Kidney	kidney
47	chr6:28258400-28273800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr6:28258600-28268600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:28258600-28273000	Weak transcription	Fetal Brain Male	brain
50	chr6:28262000-28268000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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