Variant report

Variant	rs12630101
Chromosome Location	chr3:46006158-46006159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46004092..46006174-chr3:46012049..46014737,3	K562	blood:
2	chr3:45999781..46002304-chr3:46004371..46006277,3	K562	blood:
3	chr3:46002701..46006681-chr3:46007479..46011297,4	K562	blood:
4	chr3:46000436..46002879-chr3:46005170..46007859,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1072755	1.00[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130080	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12485978	0.82[JPT][hapmap]
rs12495073	0.92[CEU][hapmap]
rs12635494	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635657	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12639598	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13060901	0.90[JPT][hapmap]
rs13066048	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13073861	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs13091821	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13091979	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1392290	0.95[JPT][hapmap]
rs1392291	0.92[ASN][1000 genomes]
rs1491959	0.82[JPT][hapmap]
rs1532071	0.83[ASN][1000 genomes]
rs1546077	0.82[JPT][hapmap]
rs1552489	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]
rs1552490	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1601867	0.85[ASN][1000 genomes]
rs17078495	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1994488	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1994489	0.83[ASN][1000 genomes]
rs1994490	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2054866	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2131091	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs2234358	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs2248228	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2291470	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2373154	0.92[CEU][hapmap]
rs35465473	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35537559	0.91[ASN][1000 genomes]
rs3733097	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3733100	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3733103	0.92[CEU][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3774634	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3774635	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3774639	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3796375	0.88[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796376	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs3821884	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3851347	0.95[JPT][hapmap]
rs4535265	1.00[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4682799	0.81[CHD][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs4682800	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4682810	0.82[JPT][hapmap]
rs4683147	0.82[CEU][hapmap]
rs4683148	0.96[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4683149	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4683152	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4683154	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4683156	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683157	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59226168	0.91[ASN][1000 genomes]
rs60539039	0.80[ASN][1000 genomes]
rs62242796	0.91[ASN][1000 genomes]
rs67044455	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6764042	0.95[JPT][hapmap]
rs6778896	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6780163	0.95[JPT][hapmap]
rs6795629	0.82[JPT][hapmap]
rs7129	0.92[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs730983	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737452	0.96[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs751552	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751553	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7623460	0.95[JPT][hapmap]
rs9311380	0.83[ASN][1000 genomes]
rs931704	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936938	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9824253	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9824886	0.89[JPT][hapmap]
rs9831315	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12630101	CDC25A	cis	cerebellum	SCAN
rs12630101	DALRD3	cis	cerebellum	SCAN
rs12630101	NCKIPSD	cis	parietal	SCAN
rs12630101	CXCR6	cis	parietal	SCAN
rs12630101	UBA7	cis	parietal	SCAN
rs12630101	SS18L2	cis	parietal	SCAN

Chromatin state (count:126 , 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	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
4	chr3:45983200-46012400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:45986200-46006800	Strong transcription	Fetal Intestine Small	intestine
6	chr3:45986200-46007600	Strong transcription	Fetal Stomach	stomach
7	chr3:45986400-46006200	Strong transcription	Fetal Muscle Leg	muscle
8	chr3:45986400-46006800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:45986400-46007600	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:45986400-46012200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:45986600-46009000	Strong transcription	Primary B cells from cord blood	blood
13	chr3:45986600-46012000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:45986800-46012200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:45987200-46013600	Strong transcription	Primary hematopoietic stem cells	blood
17	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:45987400-46026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:45987600-46007800	Strong transcription	K562	blood
20	chr3:45987800-46012200	Strong transcription	HepG2	liver
21	chr3:45987800-46026400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:45988000-46012000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr3:45988000-46026600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:45988200-46009800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:45988200-46012000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:45988800-46011800	Strong transcription	Lung	lung
29	chr3:45989400-46013800	Strong transcription	Dnd41	blood
30	chr3:45990600-46017200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr3:45991200-46006800	Strong transcription	HSMMtube	muscle
32	chr3:45991200-46012000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:45991200-46017400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr3:45991400-46009800	Strong transcription	Aorta	Aorta
35	chr3:45991400-46009800	Strong transcription	NHLF	lung
36	chr3:45992600-46013200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:45992600-46013600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:45992800-46006400	Strong transcription	Primary T cells from cord blood	blood
39	chr3:45993000-46013600	Strong transcription	Thymus	Thymus
40	chr3:45993200-46007000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:45994200-46007600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr3:45994400-46007600	Strong transcription	Adipose Nuclei	Adipose
43	chr3:45994400-46008000	Strong transcription	Placenta	Placenta
44	chr3:45995000-46007400	Strong transcription	HUVEC	blood vessel
45	chr3:45995400-46008400	Weak transcription	Fetal Brain Male	brain
46	chr3:45996200-46025400	Strong transcription	Liver	Liver
47	chr3:45998400-46009600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:45998800-46008400	Strong transcription	Colonic Mucosa	Colon
49	chr3:45999000-46008000	Strong transcription	Gastric	stomach
50	chr3:45999200-46010600	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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