Variant report

Variant	rs3796548
Chromosome Location	chr4:57259856-57259857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57256994..57259922-chr4:57269239..57271312,2	K562	blood:
2	chr4:57252534..57255192-chr4:57257421..57260881,3	MCF-7	breast:
3	chr4:57257925..57261959-chr4:57299598..57302953,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128050	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000269921	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10008223	0.84[EUR][1000 genomes]
rs10010544	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10013402	0.84[EUR][1000 genomes]
rs10434444	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1060472	0.89[TSI][hapmap]
rs11133442	0.89[TSI][hapmap]
rs11133443	1.00[CEU][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1124569	0.83[EUR][1000 genomes]
rs11723782	0.86[EUR][1000 genomes]
rs12498340	1.00[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs12501502	0.80[TSI][hapmap]
rs12645138	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1520026	0.80[TSI][hapmap]
rs17086696	1.00[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs1967559	0.83[TSI][hapmap]
rs1983378	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2030366	0.89[EUR][1000 genomes]
rs2049088	0.85[EUR][1000 genomes]
rs2271923	0.80[TSI][hapmap]
rs2271925	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510634	0.84[EUR][1000 genomes]
rs34510373	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3822001	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4493603	0.80[TSI][hapmap]
rs4565139	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4864579	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4864580	0.86[EUR][1000 genomes]
rs4865088	0.83[EUR][1000 genomes]
rs4865089	0.81[EUR][1000 genomes]
rs4865092	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs56066795	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56356367	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56672277	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56887793	0.86[EUR][1000 genomes]
rs59997251	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60104031	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61032900	0.83[EUR][1000 genomes]
rs6554344	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs67343558	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67721941	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67957495	0.83[EUR][1000 genomes]
rs6820279	0.83[EUR][1000 genomes]
rs6836118	1.00[CEU][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6853418	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73167398	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7664841	0.89[TSI][hapmap]
rs7670991	0.84[EUR][1000 genomes]
rs7693372	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7696808	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8340	1.00[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3796548	AASDH	cis	cerebellum	SCAN
rs3796548	SRP72	cis	normal skin	skin_eQTL
rs3796548	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs3796548	AASDH	cis	parietal	SCAN
rs3796548	SRP72	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57268400	Weak transcription	Lung	lung
3	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
4	chr4:57254600-57264000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:57254600-57271600	Weak transcription	Ovary	ovary
6	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
7	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:57254800-57260800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:57254800-57261800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:57254800-57262000	Weak transcription	Placenta	Placenta
11	chr4:57254800-57264000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:57254800-57264000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:57254800-57271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:57254800-57273200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
19	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
20	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:57255000-57260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:57255000-57261200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:57255000-57262200	Weak transcription	A549	lung
24	chr4:57255000-57264400	Weak transcription	Brain Germinal Matrix	brain
25	chr4:57255000-57264800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:57255000-57265600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:57255000-57266000	Weak transcription	Primary B cells from cord blood	blood
28	chr4:57255000-57266200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:57255000-57266200	Weak transcription	NH-A	brain
30	chr4:57255000-57266400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr4:57255000-57266400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:57255000-57266600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:57255000-57266600	Weak transcription	HSMM	muscle
34	chr4:57255000-57266800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:57255000-57269200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:57255000-57271400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:57255200-57262000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr4:57255200-57262200	Weak transcription	Fetal Lung	lung
39	chr4:57255200-57262200	Weak transcription	Osteobl	bone
40	chr4:57255200-57264000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:57255200-57264000	Weak transcription	Fetal Stomach	stomach
42	chr4:57255200-57266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:57255200-57266200	Weak transcription	HUVEC	blood vessel
44	chr4:57255200-57266400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr4:57255200-57266800	Weak transcription	Fetal Kidney	kidney
46	chr4:57255200-57266800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr4:57255200-57267200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:57255200-57267400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:57255200-57271600	Weak transcription	NHEK	skin
50	chr4:57255200-57272200	Weak transcription	Stomach Smooth Muscle	stomach

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