Variant report

Variant	rs4340469
Chromosome Location	chr2:189269721-189269722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189269523..189271101-chr2:189286917..189288426,2	K562	blood:
2	chr2:189243159..189245968-chr2:189269525..189271329,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10167709	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10170220	0.81[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10174928	0.81[CEU][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10179504	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10180687	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10180956	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10182377	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10185828	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10192374	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10198025	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10199264	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10204674	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10206167	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10209733	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10210696	0.82[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10211189	0.81[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10804020	0.81[YRI][hapmap]
rs10931355	0.81[CEU][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10931358	0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931359	0.88[CHD][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs1125099	0.89[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11682085	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151691	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12329399	0.81[CEU][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12465164	0.81[JPT][hapmap];0.85[YRI][hapmap]
rs12465625	0.80[JPT][hapmap];0.84[YRI][hapmap]
rs12474692	0.80[CHB][hapmap];0.87[YRI][hapmap]
rs12624002	0.81[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs12693498	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12987194	1.00[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12990374	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13384413	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13387350	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13388723	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13388746	0.81[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13389155	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13389879	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13394421	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13412312	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13415123	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13420369	0.93[CEU][hapmap];0.91[JPT][hapmap]
rs13422246	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13422836	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13423891	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13424536	0.93[JPT][hapmap]
rs13426709	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13427070	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28542209	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28564315	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3890574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4261684	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4274570	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4349309	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4361092	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4381754	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4398237	0.93[JPT][hapmap]
rs4430902	1.00[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4433962	0.81[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4458180	1.00[CEU][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4476318	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4513258	0.93[JPT][hapmap]
rs4522565	0.81[CEU][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4564741	0.83[ASN][1000 genomes]
rs4640356	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4666758	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs4667225	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4667226	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4667227	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4992744	1.00[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55693630	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56072532	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58966470	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58978246	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59206116	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60796263	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62183213	0.82[ASN][1000 genomes]
rs6434280	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66732509	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs66923332	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704814	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67086516	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67092191	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67240894	0.90[EUR][1000 genomes]
rs6725860	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727850	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6729182	0.93[JPT][hapmap]
rs6732963	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6737728	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739162	0.81[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6743120	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6743636	0.81[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6756220	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6761769	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6761785	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67750782	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67798410	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67919447	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72907672	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73040452	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7420700	0.81[CEU][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7561448	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7566619	0.81[CHD][hapmap];0.82[YRI][hapmap]
rs7574262	0.81[CHD][hapmap]
rs7579610	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7585703	0.89[YRI][hapmap]
rs7586390	0.82[YRI][hapmap]
rs7593215	0.81[CEU][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7595327	0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7595377	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7606178	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7607063	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs893745	0.85[YRI][hapmap]
rs9288157	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9808557	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv533786	chr2:189248503-189354495	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv9852	chr2:189267263-189277181	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4340469	MYO1B	cis	cerebellum	SCAN
rs4340469	COL3A1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189251000-189285200	Weak transcription	Aorta	Aorta
2	chr2:189251200-189270000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:189251200-189270200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:189256000-189270600	Weak transcription	Fetal Lung	lung
5	chr2:189261600-189270000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:189261800-189269800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:189263000-189271000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:189264000-189270200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:189264000-189283800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:189264200-189270400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:189264200-189270400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:189264400-189274200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:189268400-189270400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:189268400-189270400	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr2:189268600-189271000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr2:189268600-189279800	Weak transcription	NHLF	lung
17	chr2:189269000-189270600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:189269000-189271000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:189269200-189270200	ZNF genes & repeats	Fetal Stomach	stomach
20	chr2:189269200-189270400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:189269200-189270600	Weak transcription	Gastric	stomach
22	chr2:189269400-189269800	ZNF genes & repeats	Placenta	Placenta
23	chr2:189269400-189270200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:189269400-189270600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:189269400-189270600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:189269600-189270200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
27	chr2:189269600-189270400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:189269600-189271000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:189269600-189271200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:189269600-189271400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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