Variant report

Variant	rs12643881
Chromosome Location	chr4:110386443-110386444
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110381168..110383587-chr4:110385101..110388629,3	K562	blood:
2	chr4:110384184..110389120-chr4:110389509..110396492,10	K562	blood:
3	chr4:110384184..110386804-chr4:110389509..110391304,2	K562	blood:
4	chr4:110378967..110381063-chr4:110384891..110387405,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10488879	0.81[ASN][1000 genomes]
rs10488910	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs10516557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11098033	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11098035	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11934486	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11935440	0.85[EUR][1000 genomes]
rs11935629	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11937053	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11938593	0.85[EUR][1000 genomes]
rs11941636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942928	0.85[EUR][1000 genomes]
rs11943384	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11943430	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11944375	0.85[EUR][1000 genomes]
rs11944659	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12639832	0.85[EUR][1000 genomes]
rs12639835	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12640161	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12641472	0.92[ASN][1000 genomes]
rs12642304	0.84[EUR][1000 genomes]
rs12643844	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12644055	0.85[EUR][1000 genomes]
rs12647695	0.85[EUR][1000 genomes]
rs12648138	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12650654	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12650873	0.85[EUR][1000 genomes]
rs13128221	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17040410	0.85[EUR][1000 genomes]
rs17040446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040512	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17040519	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17585970	0.85[TSI][hapmap]
rs17619262	0.85[TSI][hapmap]
rs17619310	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs28527792	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28611124	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61439452	0.85[EUR][1000 genomes]
rs61553525	0.85[EUR][1000 genomes]
rs6533429	0.85[EUR][1000 genomes]
rs6815455	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6821051	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821221	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823032	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6825928	0.81[CHD][hapmap]
rs6851517	0.85[EUR][1000 genomes]
rs72892766	0.80[EUR][1000 genomes]
rs72896619	1.00[EUR][1000 genomes]
rs72896622	1.00[EUR][1000 genomes]
rs72896625	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72896629	1.00[EUR][1000 genomes]
rs7436745	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7440371	0.85[EUR][1000 genomes]

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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12643881	RPS4Y1	trans	lymphoblastoid	seeQTL
rs12643881	DDX3Y	trans	lymphoblastoid	seeQTL
rs12643881	KDM5D	trans	lymphoblastoid	seeQTL
rs12643881	EIF1AY	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110363600-110398400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:110366000-110391400	Weak transcription	Small Intestine	intestine
3	chr4:110371400-110393200	Weak transcription	Stomach Mucosa	stomach
4	chr4:110371600-110393400	Weak transcription	HSMMtube	muscle
5	chr4:110378800-110415800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:110382800-110390400	Strong transcription	NH-A	brain
7	chr4:110383000-110386800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:110383000-110387800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:110383000-110387800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:110383200-110386600	Strong transcription	Fetal Muscle Leg	muscle
11	chr4:110383200-110386800	Strong transcription	Primary T cells from cord blood	blood
12	chr4:110383200-110387000	Strong transcription	Fetal Intestine Large	intestine
13	chr4:110383400-110387000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:110383400-110387000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr4:110383400-110388000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:110383400-110396000	Strong transcription	Fetal Thymus	thymus
17	chr4:110383400-110397600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr4:110383600-110386800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr4:110383600-110386800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:110383600-110386800	Strong transcription	HepG2	liver
21	chr4:110383600-110386800	Strong transcription	K562	blood
22	chr4:110383600-110387000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr4:110383600-110387000	Strong transcription	Dnd41	blood
24	chr4:110383600-110387400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:110383600-110388200	Strong transcription	HUVEC	blood vessel
26	chr4:110383600-110391600	Weak transcription	Psoas Muscle	Psoas
27	chr4:110383600-110392000	Strong transcription	HSMM	muscle
28	chr4:110383800-110387000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr4:110383800-110387400	Strong transcription	Liver	Liver
30	chr4:110383800-110387400	Strong transcription	NHLF	lung
31	chr4:110383800-110387800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:110383800-110389400	Strong transcription	Primary hematopoietic stem cells	blood
33	chr4:110384000-110386600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:110384000-110386600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr4:110384000-110386800	Strong transcription	Fetal Lung	lung
36	chr4:110384000-110387000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:110384000-110387200	Strong transcription	Placenta	Placenta
38	chr4:110384000-110387400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:110384000-110387400	Strong transcription	GM12878-XiMat	blood
40	chr4:110384000-110387600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:110384000-110387600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:110384000-110388000	Strong transcription	Primary B cells from cord blood	blood
43	chr4:110384200-110386600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr4:110384200-110386800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:110384200-110387000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:110384200-110387000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr4:110384200-110387000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:110384200-110387000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr4:110384200-110387200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:110384400-110386600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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