Variant report

Variant	rs16846683
Chromosome Location	chr1:174083339-174083340
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	chr1:174073153..174074943-chr1:174081881..174084232,2	K562	blood:
2	chr1:174082792..174085808-chr1:174127455..174130130,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RC3H1-1	chr1:174083005-174084584	NONHSAT007721

Variant related genes	Relation type
ENSG00000152061	Chromatin interaction
ENSG00000227373	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10798301	0.87[CHB][hapmap]
rs10798302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10912719	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10912722	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10912747	1.00[YRI][hapmap]
rs12066153	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12076453	0.91[YRI][hapmap]
rs12076799	0.86[EUR][1000 genomes]
rs12079062	0.83[CHB][hapmap]
rs12092774	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12096785	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12563301	0.87[CHB][hapmap]
rs12563395	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568409	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376011	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884994	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1951627	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2860907	1.00[YRI][hapmap]
rs4592301	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4607949	1.00[YRI][hapmap]
rs4650945	0.83[CHB][hapmap]
rs4652169	0.87[CHB][hapmap]
rs61547493	0.82[ASN][1000 genomes]
rs61826843	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61826844	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827891	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827894	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6425273	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661868	0.97[ASN][1000 genomes]
rs6665484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6673632	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6677660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6686083	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6689285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6695327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696076	0.83[CHB][hapmap]
rs6696163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6699146	0.87[CHB][hapmap]
rs714624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7413166	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7511780	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7533430	0.83[CHB][hapmap]
rs7538312	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7553788	0.87[CHB][hapmap]
rs7554915	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174081800-174086200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:174082000-174083400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:174082200-174084000	Weak transcription	Ovary	ovary
4	chr1:174082800-174084000	Weak transcription	Fetal Heart	heart
5	chr1:174082800-174084000	Weak transcription	Stomach Smooth Muscle	stomach

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