Variant report

Variant	rs10002437
Chromosome Location	chr4:1157776-1157777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:1157568..1159327-chr4:1159533..1161126,2	MCF-7	breast:
2	chr4:1156903..1159382-chr4:1165380..1166976,2	K562	blood:
3	chr4:1157316..1159655-chr4:1161793..1164366,2	K562	blood:
4	chr4:1157301..1159863-chr4:1164074..1166976,3	K562	blood:
5	chr4:1123569..1125967-chr4:1156643..1158968,2	K562	blood:

Variant related genes	Relation type
ENSG00000159674	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10002248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015944	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027895	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029139	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032470	0.88[CEU][hapmap]
rs10033163	0.88[CEU][hapmap]
rs11247974	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724989	0.88[CEU][hapmap]
rs11726554	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11728360	0.91[AFR][1000 genomes]
rs11731685	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732057	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734374	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736950	0.90[AFR][1000 genomes]
rs13119696	1.00[CEU][hapmap]
rs13435166	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383660	0.88[CEU][hapmap]
rs1481167	1.00[CEU][hapmap]
rs17164384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28578449	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28621675	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28785628	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28855974	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28856334	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2924495	0.88[CEU][hapmap]
rs4246684	0.88[CEU][hapmap]
rs4974561	1.00[CEU][hapmap]
rs4974569	0.88[CEU][hapmap]
rs4974571	0.88[CEU][hapmap]
rs4974573	0.88[CEU][hapmap]
rs4974628	0.88[CEU][hapmap]
rs4974639	0.88[CEU][hapmap]
rs4974642	0.88[CEU][hapmap]
rs4974643	0.88[CEU][hapmap]
rs4974644	0.88[CEU][hapmap]
rs588824	0.88[CEU][hapmap]
rs589660	0.88[CEU][hapmap]
rs59465697	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604526	0.85[CEU][hapmap]
rs606327	0.88[CEU][hapmap]
rs608066	0.86[CEU][hapmap]
rs614945	0.88[CEU][hapmap]
rs615381	0.88[CEU][hapmap]
rs616569	0.88[CEU][hapmap]
rs619407	0.88[CEU][hapmap]
rs620398	0.88[CEU][hapmap]
rs629638	0.88[CEU][hapmap]
rs632319	0.88[CEU][hapmap]
rs633087	0.88[CEU][hapmap]
rs633141	0.88[CEU][hapmap]
rs633599	0.88[CEU][hapmap]
rs633954	0.88[CEU][hapmap]
rs643043	1.00[CEU][hapmap]
rs649243	0.88[CEU][hapmap]
rs649616	0.88[CEU][hapmap]
rs6599282	1.00[CEU][hapmap];0.84[MKK][hapmap]
rs6599283	1.00[CEU][hapmap];0.84[MKK][hapmap]
rs6599284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6599285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671790	0.88[CEU][hapmap]
rs6812059	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817989	0.88[CEU][hapmap]
rs681857	0.88[CEU][hapmap]
rs682243	0.88[CEU][hapmap]
rs682787	0.88[CEU][hapmap]
rs6836158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839768	0.88[CEU][hapmap]
rs6840162	0.88[CEU][hapmap]
rs73065688	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73065696	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73065698	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73067706	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73067775	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73067776	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73219741	1.00[ASN][1000 genomes]
rs7659054	0.90[MEX][hapmap]
rs7661069	0.90[MEX][hapmap]
rs7669287	0.90[MEX][hapmap]
rs7676956	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678661	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679718	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685051	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878324	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9992322	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv536980	chr4:827866-1167377	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv1004727	chr4:1015652-1158207	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv536984	chr4:1015652-1158207	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv1005990	chr4:1015652-1167619	Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
14	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
15	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10002437	ADD1	cis	cerebellum	SCAN
rs10002437	RNF212	cis	parietal	SCAN
rs10002437	RNF212	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1146600-1160800	Weak transcription	Ovary	ovary
2	chr4:1149200-1161000	Weak transcription	Right Atrium	heart
3	chr4:1149600-1160800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:1149600-1161000	Weak transcription	Gastric	stomach
5	chr4:1151200-1157800	Weak transcription	Pancreas	Pancrea
6	chr4:1155600-1160400	Weak transcription	Colonic Mucosa	Colon
7	chr4:1156200-1158400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr4:1156200-1158800	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:1156600-1158000	Enhancers	Primary B cells from cord blood	blood
10	chr4:1156600-1160400	Weak transcription	Liver	Liver
11	chr4:1156600-1160800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:1157000-1158000	Enhancers	K562	blood
13	chr4:1157000-1158000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr4:1157000-1158800	ZNF genes & repeats	GM12878-XiMat	blood
15	chr4:1157200-1160800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:1157400-1157800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:1157600-1160800	Weak transcription	Stomach Mucosa	stomach

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