Variant report

Variant	rs1552489
Chromosome Location	chr3:45993973-45993974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:45992659..45994641-chr3:46028942..46030792,2	K562	blood:
2	chr3:45992876..45995243-chr3:45997512..46000332,2	K562	blood:
3	chr3:45992901..45995659-chr3:45998923..46000689,2	K562	blood:

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1072755	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130080	0.96[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12495073	0.92[CEU][hapmap]
rs12630101	1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12635494	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12635657	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12639598	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13066048	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13073861	0.84[CEU][hapmap]
rs13091821	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13091979	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1392291	0.81[ASN][1000 genomes]
rs1532071	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1552490	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1601867	0.98[ASN][1000 genomes]
rs17078449	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs17078495	0.80[EUR][1000 genomes]
rs1994488	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994489	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1994490	0.83[CHD][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs2054866	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2131091	0.84[CEU][hapmap]
rs2171530	0.82[ASN][1000 genomes]
rs2234358	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs2248228	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291470	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2373154	0.92[CEU][hapmap]
rs35465473	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733100	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs3733103	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3774634	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3774635	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3774638	0.86[CHB][hapmap]
rs3774639	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796373	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs3796375	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821884	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs4535265	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4682799	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4682800	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs4683147	0.82[CEU][hapmap]
rs4683148	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683149	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683152	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683154	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683156	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683157	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62242787	0.81[ASN][1000 genomes]
rs67044455	0.80[EUR][1000 genomes]
rs6778896	0.83[EUR][1000 genomes]
rs6781121	0.81[CHB][hapmap]
rs6800954	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs7129	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs730983	0.96[CEU][hapmap]
rs737452	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs751552	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs751553	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9311380	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs936938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs936939	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs9824253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9831315	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1552489	SS18L2	cis	parietal	SCAN
rs1552489	DALRD3	cis	cerebellum	SCAN
rs1552489	UBA7	cis	parietal	SCAN
rs1552489	CXCR6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:45981000-45999400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
6	chr3:45982200-45999800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr3:45982800-46000800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:45983200-46012400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:45984000-45994000	Weak transcription	HMEC	breast
10	chr3:45984200-45994200	Strong transcription	Liver	Liver
11	chr3:45984400-45998200	Strong transcription	Left Ventricle	heart
12	chr3:45984400-46000800	Weak transcription	Psoas Muscle	Psoas
13	chr3:45986200-45998200	Strong transcription	Brain Substantia Nigra	brain
14	chr3:45986200-46006800	Strong transcription	Fetal Intestine Small	intestine
15	chr3:45986200-46007600	Strong transcription	Fetal Stomach	stomach
16	chr3:45986400-45997000	Strong transcription	Pancreas	Pancrea
17	chr3:45986400-45997200	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr3:45986400-46001400	Weak transcription	A549	lung
19	chr3:45986400-46006200	Strong transcription	Fetal Muscle Leg	muscle
20	chr3:45986400-46006800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:45986400-46007600	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:45986400-46012200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:45986600-45997000	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr3:45986600-45997000	Strong transcription	Brain Angular Gyrus	brain
26	chr3:45986600-45997400	Strong transcription	Brain Cingulate Gyrus	brain
27	chr3:45986600-46009000	Strong transcription	Primary B cells from cord blood	blood
28	chr3:45986600-46012000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:45986800-46012200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:45987000-45997600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:45987200-46013600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:45987400-46026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:45987600-45998200	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr3:45987600-46002000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:45987600-46007800	Strong transcription	K562	blood
38	chr3:45987800-45995600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:45987800-45997400	Strong transcription	Brain Anterior Caudate	brain
40	chr3:45987800-45997600	Strong transcription	Brain Hippocampus Middle	brain
41	chr3:45987800-46001400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:45987800-46012200	Strong transcription	HepG2	liver
43	chr3:45987800-46026400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:45988000-45994200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:45988000-45997000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:45988000-45997000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:45988000-45997600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:45988000-45999400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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