Variant report

Variant	rs4678447
Chromosome Location	chr3:136555433-136555434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136548915..136551546-chr3:136552798..136555438,3	K562	blood:
2	chr3:136554235..136556505-chr3:136559214..136561778,2	K562	blood:
3	chr3:136554139..136557282-chr3:136559965..136563273,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10470440	0.81[MKK][hapmap]
rs1052618	0.91[LWK][hapmap];0.81[MKK][hapmap]
rs10804645	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs108858	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs10935198	0.81[AFR][1000 genomes]
rs11711599	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11717974	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12054220	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12497379	0.81[AFR][1000 genomes]
rs12629000	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077864	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095028	0.90[CHD][hapmap]
rs1406539	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569228	0.91[LWK][hapmap];0.81[AFR][1000 genomes]
rs16844241	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171519	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1965107	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2176270	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361232	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs361233	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs361235	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs361238	1.00[CHB][hapmap]
rs361240	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs361253	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4678271	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4678275	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62410363	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62410438	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71630059	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7630571	0.80[AMR][1000 genomes]
rs7631541	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs7648198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7648817	0.93[LWK][hapmap]
rs835636	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs835637	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs835652	0.86[CHB][hapmap]
rs9682783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9818397	0.93[LWK][hapmap];0.81[AFR][1000 genomes]
rs9819572	0.93[LWK][hapmap];0.81[AFR][1000 genomes]
rs9828009	0.93[LWK][hapmap];0.81[MKK][hapmap]
rs9835096	0.81[AFR][1000 genomes]
rs9845076	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs9845460	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
2	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv877533	chr3:136539689-136662954	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4678447	NCK1	cis	parietal	SCAN
rs4678447	TMEM22	cis	cerebellum	SCAN
rs4678447	MSL2	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136550600-136558400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:136550800-136561000	Weak transcription	Thymus	Thymus
3	chr3:136551000-136557600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:136551600-136574000	Weak transcription	HepG2	liver
5	chr3:136552400-136557400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:136552400-136570800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:136552600-136558000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:136552600-136579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:136553400-136555800	Enhancers	Primary hematopoietic stem cells	blood
10	chr3:136553400-136556800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:136553400-136557600	Enhancers	HUVEC	blood vessel
12	chr3:136553400-136558000	Weak transcription	Fetal Thymus	thymus
13	chr3:136553400-136560200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:136553800-136555600	Enhancers	NHLF	lung
15	chr3:136553800-136555800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:136553800-136557600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:136554000-136558000	Weak transcription	Primary B cells from cord blood	blood
18	chr3:136554200-136556000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:136554200-136556000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr3:136554200-136556200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:136554200-136556200	Enhancers	NHDF-Ad	bronchial
22	chr3:136554200-136561000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:136554400-136555600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:136554400-136555600	Enhancers	Adipose Nuclei	Adipose
25	chr3:136554400-136555600	Enhancers	Brain Angular Gyrus	brain
26	chr3:136554400-136557200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:136554400-136557400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:136554600-136555600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:136554600-136555600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr3:136554600-136555600	Enhancers	NH-A	brain
31	chr3:136554600-136555600	Enhancers	Osteobl	bone
32	chr3:136554600-136555800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:136554600-136555800	Enhancers	Colon Smooth Muscle	Colon
34	chr3:136554600-136555800	Enhancers	Right Ventricle	heart
35	chr3:136554600-136555800	Enhancers	HSMMtube	muscle
36	chr3:136554600-136556200	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:136554600-136556400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:136554600-136557200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:136554600-136557400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:136554600-136559400	Enhancers	Fetal Brain Male	brain
41	chr3:136554800-136555600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:136554800-136555600	Enhancers	Right Atrium	heart
43	chr3:136554800-136555600	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr3:136554800-136557200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:136554800-136557400	Weak transcription	Hela-S3	cervix
46	chr3:136554800-136557600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:136554800-136578400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:136554800-136579400	Weak transcription	Fetal Lung	lung
49	chr3:136555000-136555600	Enhancers	Brain Anterior Caudate	brain
50	chr3:136555000-136555800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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