Variant report

Variant	rs6928440
Chromosome Location	chr6:53826707-53826708
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53819656..53822349-chr6:53824906..53826764,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10456168	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10456676	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10755768	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10948790	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12190914	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13437448	0.94[ASN][1000 genomes]
rs2006013	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206574	0.82[ASN][1000 genomes]
rs2397150	0.82[ASN][1000 genomes]
rs34299171	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4398734	0.86[ASN][1000 genomes]
rs4712050	0.89[ASN][1000 genomes]
rs4712051	0.90[ASN][1000 genomes]
rs5006063	0.95[ASN][1000 genomes]
rs6458973	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6902746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906326	0.81[CEU][hapmap]
rs6907354	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6909052	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6909056	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6909350	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6927232	0.92[ASN][1000 genomes]
rs6935942	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs742525	0.86[ASN][1000 genomes]
rs7744962	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7752981	0.82[ASN][1000 genomes]
rs7769351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296727	0.94[ASN][1000 genomes]
rs9357777	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9357779	0.81[ASN][1000 genomes]
rs9367545	0.91[AMR][1000 genomes]
rs9367546	0.82[ASN][1000 genomes]
rs9370245	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9395890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9395891	1.00[CEU][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395892	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9395893	0.86[ASN][1000 genomes]
rs9395894	0.86[ASN][1000 genomes]
rs9463996	0.80[CEU][hapmap]
rs9463997	0.81[CEU][hapmap];0.80[TSI][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6928440	DEFB110	cis	cerebellum	SCAN
rs6928440	LRRC1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53819000-53827000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53824800-53827000	Enhancers	HSMMtube	muscle
3	chr6:53824800-53827800	Enhancers	HSMM	muscle
4	chr6:53825200-53827000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:53825200-53827200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:53825400-53827000	Weak transcription	Osteobl	bone
7	chr6:53825400-53827600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:53825800-53827200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:53826200-53828400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:53826400-53827000	Enhancers	Brain Germinal Matrix	brain
11	chr6:53826400-53827400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:53826400-53827400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:53826400-53827400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr6:53826400-53827800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:53826600-53826800	Enhancers	NH-A	brain
16	chr6:53826600-53827200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr6:53826600-53827400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:53826600-53827400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:53826600-53827400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr6:53826600-53827400	Enhancers	HMEC	breast
21	chr6:53826600-53827800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr6:53826600-53827800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr6:53826600-53827800	Enhancers	Placenta	Placenta
24	chr6:53826600-53828200	Enhancers	Fetal Heart	heart

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