Variant report

Variant	rs6425275
Chromosome Location	chr1:174122088-174122089
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	chr1:174030314..174033290-chr1:174119943..174122935,2	K562	blood:
2	chr1:174120725..174126684-chr1:174127143..174130813,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227373	Chromatin interaction
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10798301	0.87[CHB][hapmap]
rs10798302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs10912719	0.82[EUR][1000 genomes]
rs10912722	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10912747	1.00[YRI][hapmap]
rs12066153	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12076453	0.91[YRI][hapmap]
rs12076799	0.85[EUR][1000 genomes]
rs12079062	0.83[CHB][hapmap]
rs12092774	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12096785	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12563301	0.87[CHB][hapmap]
rs12563395	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568409	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13376011	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16846683	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]
rs1884994	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2860907	1.00[YRI][hapmap]
rs4592301	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4607949	1.00[YRI][hapmap]
rs4650945	0.83[CHB][hapmap]
rs4652169	0.87[CHB][hapmap]
rs61826843	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826844	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61827891	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61827894	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425273	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6661868	0.93[ASN][1000 genomes]
rs6665484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6677660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[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];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6695327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696076	0.83[CHB][hapmap]
rs6696163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6699146	0.87[CHB][hapmap]
rs714624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7413166	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7511780	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7533430	0.83[CHB][hapmap]
rs7538312	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7553788	0.87[CHB][hapmap]
rs7554915	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174120000-174128000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:174121000-174123400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:174121200-174123200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:174121200-174123400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:174121400-174122200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:174121400-174123000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:174121400-174123400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:174121400-174123400	Enhancers	NHEK	skin
9	chr1:174121600-174122400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:174121600-174122800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:174121600-174122800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr1:174121600-174123000	Enhancers	Primary T cells from cord blood	blood
13	chr1:174121600-174123200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:174121600-174123200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:174121600-174123200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr1:174121600-174123200	Enhancers	HMEC	breast
17	chr1:174121600-174123400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:174121600-174123400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:174121600-174123400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:174121600-174123600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr1:174121600-174124000	Enhancers	GM12878-XiMat	blood
22	chr1:174121800-174122600	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:174121800-174122800	Enhancers	A549	lung
24	chr1:174121800-174123200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:174121800-174123600	Enhancers	K562	blood
26	chr1:174122000-174122200	Enhancers	Hela-S3	cervix
27	chr1:174122000-174123200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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