Variant report

Variant	rs1568693
Chromosome Location	chr4:8392194-8392195
allele	C/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	EP300	chr4:8392024-8392437	SK-N-SH_RA	brain:	n/a	n/a
2	GATA2	chr4:8392094-8392440	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
RNA5SP152	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10016221	0.92[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs10017177	0.96[ASN][1000 genomes]
rs1006113	0.98[ASN][1000 genomes]
rs10938710	0.87[ASN][1000 genomes]
rs10938712	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11721377	0.91[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs11724408	0.94[ASN][1000 genomes]
rs11731308	0.96[ASN][1000 genomes]
rs11931965	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934603	0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs11938364	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs13103946	0.94[ASN][1000 genomes]
rs13107329	0.94[ASN][1000 genomes]
rs13130336	0.94[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13134272	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs13136987	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs13139522	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs13150818	0.93[ASN][1000 genomes]
rs1403580	0.82[AFR][1000 genomes]
rs1568692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242483	0.84[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2293229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293230	1.00[ASW][hapmap];0.92[LWK][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs2386119	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs28541824	0.86[AFR][1000 genomes]
rs28637781	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28805000	0.94[ASN][1000 genomes]
rs34947973	0.93[ASN][1000 genomes]
rs35893558	0.93[ASN][1000 genomes]
rs3796740	0.92[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs3796747	0.85[YRI][hapmap];0.90[AFR][1000 genomes]
rs3796749	0.91[AFR][1000 genomes]
rs3822207	1.00[ASW][hapmap];0.92[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes]
rs4543095	0.92[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs6447868	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73087705	0.97[ASN][1000 genomes]
rs7668735	0.98[ASN][1000 genomes]
rs7696306	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs7697154	1.00[ASW][hapmap];0.88[LWK][hapmap];0.82[MKK][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs9291391	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9291392	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs940135	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs950306	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv878609	chr4:8373832-8407406	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv878610	chr4:8377058-8416976	ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	esv1005399	chr4:8387281-8397983	Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1568693	C4orf23	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8360400-8394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:8360400-8395600	Weak transcription	NHEK	skin
3	chr4:8362000-8395400	Weak transcription	Fetal Brain Male	brain
4	chr4:8364800-8392400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:8366400-8411600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:8373400-8401600	Strong transcription	Fetal Intestine Small	intestine
7	chr4:8375000-8401600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:8378600-8398600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:8378600-8398800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:8378800-8397800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:8379000-8395400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:8381000-8393800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:8381600-8392400	Strong transcription	Brain Cingulate Gyrus	brain
14	chr4:8381800-8394400	Strong transcription	Brain Germinal Matrix	brain
15	chr4:8381800-8398600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:8382400-8401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:8383800-8419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:8384000-8394600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:8384000-8395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:8384000-8399600	Strong transcription	Spleen	Spleen
21	chr4:8384800-8401600	Strong transcription	Thymus	Thymus
22	chr4:8384800-8418600	Strong transcription	Primary T cells from cord blood	blood
23	chr4:8385200-8395200	Weak transcription	Fetal Kidney	kidney
24	chr4:8385200-8411600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:8385400-8395600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:8385600-8392400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr4:8385600-8407000	Weak transcription	Stomach Mucosa	stomach
28	chr4:8386000-8393400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:8386200-8392200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:8386400-8392400	Weak transcription	GM12878-XiMat	blood
31	chr4:8386400-8393000	Strong transcription	Fetal Stomach	stomach
32	chr4:8386400-8398200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:8386400-8408400	Strong transcription	Fetal Intestine Large	intestine
34	chr4:8386600-8393400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:8386600-8398600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:8386600-8399400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr4:8386600-8400600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:8386800-8393000	Strong transcription	Adipose Nuclei	Adipose
39	chr4:8386800-8393000	Strong transcription	Rectal Smooth Muscle	rectum
40	chr4:8386800-8396600	Strong transcription	Lung	lung
41	chr4:8387000-8392800	Strong transcription	Brain Anterior Caudate	brain
42	chr4:8387200-8392800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:8387200-8394600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr4:8387200-8395000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:8387200-8395600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:8387400-8392200	Weak transcription	Fetal Heart	heart
47	chr4:8387400-8392800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:8387400-8393000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:8387400-8399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr4:8387400-8412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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