Variant report

Variant	rs1443100
Chromosome Location	chr3:105568376-105568377
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105567530..105570429-chr3:105573055..105575422,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD47-8	chr3:105565135-105569968	NONHSAT090970

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12054270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487349	0.82[ASN][1000 genomes]
rs12493071	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1503923	0.87[AMR][1000 genomes]
rs16851512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851705	0.87[AMR][1000 genomes]
rs16851706	0.87[AMR][1000 genomes]
rs16851707	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1814078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120103	1.00[CEU][hapmap]
rs2120104	0.88[ASN][1000 genomes]
rs2301028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3213928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34360428	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35909361	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772517	0.90[ASN][1000 genomes]
rs3772522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3772525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821490	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4431143	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4469007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255570	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255571	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255572	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255573	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255575	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62256353	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62258160	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261460	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261462	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261487	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261489	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261491	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261492	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261493	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261495	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261496	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261497	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261498	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261499	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261538	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261539	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263056	0.87[ASN][1000 genomes]
rs62263057	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62263059	0.87[ASN][1000 genomes]
rs62263169	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263170	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264260	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6809776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7619706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7628896	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7631219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641527	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964173	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9657903	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9657924	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs971109	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849559	0.88[ASN][1000 genomes]
rs9856147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105533800-105570000	Weak transcription	Dnd41	blood
2	chr3:105540800-105569600	Weak transcription	Fetal Thymus	thymus
3	chr3:105543400-105581200	Weak transcription	Gastric	stomach
4	chr3:105543800-105571000	Weak transcription	Lung	lung
5	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
7	chr3:105549000-105571800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:105550000-105569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:105555800-105576600	Weak transcription	Psoas Muscle	Psoas
10	chr3:105556200-105570200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:105556200-105571600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr3:105556200-105579000	Weak transcription	Stomach Mucosa	stomach
13	chr3:105556600-105569600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:105556600-105569800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:105557800-105579200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:105558200-105571800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:105561600-105569600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:105561600-105569600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:105561600-105569600	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:105561800-105569800	Weak transcription	HSMMtube	muscle
24	chr3:105562000-105586000	Weak transcription	K562	blood
25	chr3:105562600-105568400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:105562600-105568800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr3:105562600-105568800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr3:105563000-105569600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:105563000-105584600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:105563200-105569400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:105563200-105569600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:105563200-105569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:105563200-105569600	Weak transcription	Liver	Liver
35	chr3:105563200-105569600	Weak transcription	Left Ventricle	heart
36	chr3:105563200-105571600	Weak transcription	Fetal Intestine Small	intestine
37	chr3:105563200-105572000	Weak transcription	HUVEC	blood vessel
38	chr3:105563200-105572200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:105563400-105569600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:105563400-105570200	Weak transcription	Fetal Brain Female	brain
41	chr3:105563400-105583000	Weak transcription	Spleen	Spleen
42	chr3:105563600-105568400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr3:105563600-105568800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:105563800-105584400	Weak transcription	Brain Angular Gyrus	brain
45	chr3:105564600-105569600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:105564600-105569800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:105564800-105569600	Weak transcription	HepG2	liver
48	chr3:105564800-105585000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:105565000-105569800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:105565000-105570000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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