Variant report

Variant	rs4653996
Chromosome Location	chr1:224373608-224373609
allele	G/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	POLR2A	chr1:224373516-224374146	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:224373581-224374082	K562	blood:	n/a	n/a
3	POLR2A	chr1:224373405-224374168	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:224372767-224373649	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:224373428-224373702	GM12878	blood:	n/a	n/a
6	WRNIP1	chr1:224373496-224373810	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:224373395-224374211	GM12892	blood:	n/a	n/a
8	MTA3	chr1:224373484-224374273	GM12878	blood:	n/a	n/a
9	SPI1	chr1:224373606-224374252	GM12878	blood:	n/a	chr1:224374024-224374033

No.	Distal block	Cell Line	Cell type
1	chr1:224300672..224304210-chr1:224370293..224374026,4	K562	blood:
2	chr1:224368636..224372565-chr1:224373050..224376148,4	MCF-7	breast:
3	chr1:224372056..224374246-chr1:224379708..224382000,2	MCF-7	breast:

Variant related genes	Relation type
DEGS1	TF binding region
ENSG00000143756	Chromatin interaction
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10916470	0.88[CEU][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11810089	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2139155	0.85[CEU][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2176600	0.82[GIH][hapmap];0.87[JPT][hapmap]
rs2405304	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36086207	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826414	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6666295	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6689187	0.88[GIH][hapmap];0.83[MEX][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	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv8857	chr1:224359943-224383023	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4653996	RAB3GAP2	cis	parietal	SCAN
rs4653996	DEGS1	cis	multi-tissue	Pritchard
rs4653996	FBXO28	cis	lymphoblastoid	seeQTL
rs4653996	DEGS1	cis	cerebellum	SCAN
rs4653996	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4653996	FBXO28	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224372000-224374000	Enhancers	Pancreas	Pancrea
2	chr1:224372000-224374000	Enhancers	Spleen	Spleen
3	chr1:224372200-224373800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:224372200-224374000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:224372200-224374000	Enhancers	Right Ventricle	heart
6	chr1:224372200-224374200	Enhancers	Primary B cells from cord blood	blood
7	chr1:224372200-224374400	Enhancers	Gastric	stomach
8	chr1:224372200-224375000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:224372200-224377200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:224372200-224377400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:224372200-224377400	Weak transcription	Fetal Intestine Large	intestine
12	chr1:224372400-224373800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr1:224372400-224373800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:224372400-224373800	Enhancers	Brain Hippocampus Middle	brain
15	chr1:224372400-224373800	Enhancers	Fetal Brain Male	brain
16	chr1:224372400-224373800	Enhancers	Fetal Heart	heart
17	chr1:224372400-224374200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:224372400-224374200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:224372400-224374400	Weak transcription	HepG2	liver
20	chr1:224372400-224375800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr1:224372400-224377400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:224372400-224379600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:224372400-224380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:224372400-224381000	Weak transcription	HSMMtube	muscle
25	chr1:224372400-224389200	Weak transcription	Fetal Kidney	kidney
26	chr1:224372600-224373800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:224372600-224373800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:224372600-224373800	Enhancers	Esophagus	oesophagus
29	chr1:224372600-224373800	Genic enhancers	Fetal Brain Female	brain
30	chr1:224372600-224373800	Enhancers	Right Atrium	heart
31	chr1:224372600-224374000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:224372600-224374000	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:224372600-224374400	Weak transcription	Liver	Liver
34	chr1:224372600-224375000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:224372600-224375200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:224372600-224375200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:224372600-224375400	Enhancers	Left Ventricle	heart
38	chr1:224372600-224377400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:224372600-224377400	Weak transcription	NH-A	brain
40	chr1:224372600-224379000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:224372600-224379600	Weak transcription	HMEC	breast
42	chr1:224372600-224380000	Weak transcription	Thymus	Thymus
43	chr1:224372600-224391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:224372600-224392400	Weak transcription	Ovary	ovary
45	chr1:224372600-224392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:224372800-224373800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:224372800-224374000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:224372800-224374200	Flanking Active TSS	GM12878-XiMat	blood
49	chr1:224372800-224374400	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr1:224372800-224374600	Genic enhancers	Primary B cells from peripheral blood	blood

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