Variant report

Variant	rs11940728
Chromosome Location	chr4:10298683-10298684
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr4:10298361-10298691	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr4:10298319-10298686	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:10298581..10300458-chr4:10305111..10307586,2	K562	blood:
2	chr4:10278587..10280479-chr4:10297418..10299087,2	K562	blood:
3	chr4:10119318..10121113-chr4:10298083..10300540,2	K562	blood:

Variant related genes	Relation type
ENSG00000251278	TF binding region
ENSG00000251338	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10012795	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10024447	0.94[ASW][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap]
rs10938749	0.93[EUR][1000 genomes]
rs11937853	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12649529	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12650204	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16894053	0.81[TSI][hapmap]
rs16894555	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs16895631	0.89[CEU][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16895909	0.94[EUR][1000 genomes]
rs16896291	0.94[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs17480130	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2024277	0.93[EUR][1000 genomes]
rs28462089	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4311315	0.82[GIH][hapmap];0.89[MEX][hapmap]
rs4530622	0.93[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs62286326	0.87[EUR][1000 genomes]
rs62286327	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62288092	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6824256	0.90[EUR][1000 genomes]
rs6835189	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes]
rs6853389	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs714086	0.88[EUR][1000 genomes]
rs714814	0.94[CEU][hapmap]
rs73224436	0.91[EUR][1000 genomes]
rs968997	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9884575	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9994391	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878681	chr4:9802853-10397327	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
2	nsv997941	chr4:9805223-10493388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
3	nsv1008649	chr4:9805223-10589802	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv1000587	chr4:9805223-10610752	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
5	nsv537022	chr4:9805223-10610752	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
6	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
7	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
8	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
9	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
10	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
11	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
12	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
13	esv2752052	chr4:9911872-10313111	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
14	nsv1010620	chr4:9937123-10686682	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
15	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
16	nsv532706	chr4:9948018-10451450	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
17	nsv878691	chr4:9966477-10418078	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
18	nsv1013487	chr4:9972011-10320963	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
19	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
20	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
21	nsv593695	chr4:10138470-10345548	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
22	nsv1000177	chr4:10212245-10557776	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
23	nsv537037	chr4:10212245-10557776	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
24	nsv1007206	chr4:10229982-10362490	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
25	nsv1013852	chr4:10287118-10320963	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
26	nsv963589	chr4:10288617-10325163	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
27	nsv1011107	chr4:10290726-10324361	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11940728	GPR78	cis	parietal	SCAN
rs11940728	PSAPL1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10297000-10299000	Enhancers	HMEC	breast
2	chr4:10297200-10298800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:10297200-10299600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr4:10297200-10299800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:10297400-10300000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:10298000-10298800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:10298000-10299000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:10298000-10299000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:10298000-10299000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:10298000-10299000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:10298000-10299000	Enhancers	NHEK	skin
12	chr4:10298000-10299200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:10298200-10298800	Enhancers	Fetal Heart	heart
14	chr4:10298200-10299000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:10298200-10299000	Enhancers	HSMMtube	muscle
16	chr4:10298200-10299400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr4:10298200-10299600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:10298400-10298800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr4:10298400-10298800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr4:10298400-10298800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr4:10298400-10298800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:10298400-10298800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:10298400-10298800	Enhancers	Gastric	stomach
24	chr4:10298400-10299000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr4:10298400-10299400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:10298400-10299400	Enhancers	Fetal Brain Female	brain
27	chr4:10298400-10299600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr4:10298400-10300000	Enhancers	Brain Substantia Nigra	brain
29	chr4:10298600-10298800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr4:10298600-10298800	Enhancers	Brain Hippocampus Middle	brain
31	chr4:10298600-10299000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:10298600-10299000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:10298600-10299000	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr4:10298600-10299200	Enhancers	Brain Cingulate Gyrus	brain
35	chr4:10298600-10299800	Enhancers	Brain Anterior Caudate	brain

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