Variant report

Variant	rs4678275
Chromosome Location	chr3:136653683-136653684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136649399..136652137-chr3:136652248..136655510,3	MCF-7	breast:
2	chr3:136652282..136654491-chr3:136657095..136659566,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10470440	0.82[MKK][hapmap]
rs1052618	0.91[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap]
rs10804645	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs108858	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs11711599	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11717974	0.88[ASN][1000 genomes]
rs12054220	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12629000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077864	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13095028	0.90[CHD][hapmap]
rs1344790	0.81[MEX][hapmap]
rs1406539	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]
rs1406540	0.81[MEX][hapmap]
rs1433318	0.81[MEX][hapmap]
rs1569228	0.91[LWK][hapmap];0.81[MEX][hapmap]
rs16844241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs171519	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1805300	0.81[MEX][hapmap]
rs1914048	0.81[MEX][hapmap]
rs1965107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965108	0.82[AFR][1000 genomes]
rs1971788	0.80[AFR][1000 genomes]
rs2031029	0.81[MEX][hapmap]
rs2043365	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2176270	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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]
rs3772388	0.81[MEX][hapmap]
rs4678271	0.92[ASN][1000 genomes]
rs4678447	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	0.92[ASN][1000 genomes]
rs62410438	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414337	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6439663	0.81[MEX][hapmap]
rs6439664	0.81[MEX][hapmap]
rs6439672	0.81[MEX][hapmap]
rs6766755	0.81[MEX][hapmap]
rs6783999	0.81[MEX][hapmap]
rs6786302	0.81[MEX][hapmap]
rs6800032	0.80[AMR][1000 genomes]
rs71630059	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610507	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7631541	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]
rs7636956	0.80[AMR][1000 genomes]
rs7645773	0.81[MEX][hapmap]
rs7648198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7648817	0.93[LWK][hapmap];0.80[MEX][hapmap];0.82[AFR][1000 genomes]
rs7651644	0.82[AFR][1000 genomes]
rs835636	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs835637	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs835652	0.86[CHB][hapmap]
rs9682106	0.81[MEX][hapmap]
rs9682783	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9815771	0.81[MEX][hapmap]
rs9818397	0.93[LWK][hapmap]
rs9819572	0.93[LWK][hapmap];0.81[MEX][hapmap]
rs9828009	0.93[LWK][hapmap];0.82[MKK][hapmap]
rs9833952	0.81[MEX][hapmap]
rs9836807	0.81[MEX][hapmap]
rs9842577	0.81[MEX][hapmap]
rs9845076	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs9845460	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];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846691	0.81[MEX][hapmap]
rs9860774	0.81[MEX][hapmap]
rs9878367	0.81[MEX][hapmap];0.80[AMR][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	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
2	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
3	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
rs4678275	MSL2	cis	cerebellum	SCAN
rs4678275	NCK1	cis	parietal	SCAN
rs4678275	TMEM22	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136619200-136656800	Weak transcription	NHLF	lung
2	chr3:136624200-136664400	Weak transcription	Aorta	Aorta
3	chr3:136626000-136661600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:136626600-136661000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:136632600-136657000	Weak transcription	HepG2	liver
6	chr3:136633800-136660200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:136634800-136656800	Weak transcription	NH-A	brain
8	chr3:136635000-136656600	Weak transcription	K562	blood
9	chr3:136637600-136661400	Weak transcription	Left Ventricle	heart
10	chr3:136638800-136664400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:136639000-136664400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:136640400-136655000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:136641000-136670000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:136641800-136656200	Weak transcription	HUVEC	blood vessel
15	chr3:136643800-136655400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:136643800-136661400	Weak transcription	Small Intestine	intestine
17	chr3:136644600-136656800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:136645000-136655400	Weak transcription	Fetal Brain Female	brain
19	chr3:136645400-136664200	Weak transcription	Placenta	Placenta
20	chr3:136645800-136664600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:136646200-136660000	Weak transcription	Lung	lung
22	chr3:136646200-136664400	Weak transcription	Ovary	ovary
23	chr3:136646600-136673800	Weak transcription	Pancreas	Pancrea
24	chr3:136647400-136655400	Weak transcription	Fetal Kidney	kidney
25	chr3:136647600-136655200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:136647600-136655800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:136647600-136657600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:136647600-136660800	Weak transcription	Thymus	Thymus
29	chr3:136647600-136661000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:136647600-136664400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:136647800-136655200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:136648000-136655400	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:136648200-136657200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:136648600-136654800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:136648600-136655400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:136648600-136673800	Weak transcription	Fetal Intestine Small	intestine
37	chr3:136649000-136661200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:136650200-136655200	Weak transcription	Fetal Lung	lung
39	chr3:136650200-136655400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:136650200-136655400	Weak transcription	Fetal Intestine Large	intestine
41	chr3:136650200-136655400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:136650200-136666600	Weak transcription	Brain Angular Gyrus	brain
43	chr3:136650200-136669400	Weak transcription	Colonic Mucosa	Colon
44	chr3:136650400-136656600	Weak transcription	Osteobl	bone
45	chr3:136650600-136655200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:136650600-136655200	Weak transcription	HSMM	muscle
47	chr3:136650600-136656600	Weak transcription	NHDF-Ad	bronchial
48	chr3:136650800-136655800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:136650800-136661400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:136650800-136664400	Weak transcription	Stomach Smooth Muscle	stomach

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