Variant report

Variant	rs7605609
Chromosome Location	chr2:178534942-178534943
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178533626..178535228-chr2:178535564..178538374,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10167783	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1047884	0.94[JPT][hapmap]
rs11678875	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11682717	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11682753	0.80[ASN][1000 genomes]
rs11890088	0.84[ASN][1000 genomes]
rs12467363	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12469884	0.85[ASN][1000 genomes]
rs12471621	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12475108	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12611503	0.86[ASN][1000 genomes]
rs12612481	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12616259	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12618542	0.87[ASW][hapmap];0.84[LWK][hapmap]
rs12990878	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12994392	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12997716	0.82[ASN][1000 genomes]
rs13008833	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13008857	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13009207	0.89[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[ASN][1000 genomes]
rs13020788	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs13034781	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1358328	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1405714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1405717	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1405718	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1527401	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1527406	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1527407	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1530034	0.85[JPT][hapmap]
rs1544002	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2222711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2365619	0.87[ASW][hapmap];0.84[LWK][hapmap]
rs3770005	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770007	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3770008	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3770009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770010	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821006	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4144275	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4144276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4337505	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4470372	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4893838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4893969	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs55792594	0.84[ASN][1000 genomes]
rs6433684	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6734426	0.87[ASW][hapmap];0.84[LWK][hapmap]
rs6734528	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs6736390	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7578325	0.92[ASN][1000 genomes]
rs7594362	0.85[ASN][1000 genomes]
rs7605493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7605757	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs880897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs880898	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs880899	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7605609	TTC30A	cis	Lymphoblastoid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178531400-178535800	Weak transcription	GM12878-XiMat	blood
2	chr2:178531400-178540000	Weak transcription	K562	blood
3	chr2:178531800-178535000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:178532800-178537000	Enhancers	Fetal Kidney	kidney
5	chr2:178532800-178538000	Weak transcription	HSMM	muscle
6	chr2:178533400-178535800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:178533800-178536600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
8	chr2:178533800-178536600	Enhancers	Dnd41	blood
9	chr2:178534000-178537200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:178534200-178535400	Enhancers	Liver	Liver
11	chr2:178534200-178537000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:178534400-178537400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
13	chr2:178534800-178535000	Enhancers	Right Atrium	heart
14	chr2:178534800-178535000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr2:178534800-178536000	Enhancers	Psoas Muscle	Psoas
16	chr2:178534800-178536200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:178534800-178536200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:178534800-178537000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:178534800-178537000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:178534800-178537200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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