Variant report

Variant	rs7754673
Chromosome Location	chr6:142331132-142331133
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142329102..142331805-chr7:35011843..35013358,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173852	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10428764	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11964559	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1336271	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1414745	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1414749	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1414750	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17054023	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17071309	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17071311	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17071313	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17071318	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17071354	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17071356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17071362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17071365	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17071369	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17071371	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1932631	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2152587	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2152588	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2184733	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4275079	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4478421	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58768480	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60224718	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6570487	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907237	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6918829	1.00[EUR][1000 genomes]
rs73777114	1.00[EUR][1000 genomes]
rs7742103	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7750642	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7764255	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029504	chr6:142131846-142333198	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv538458	chr6:142131846-142333198	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1017195	chr6:142142454-142336722	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv604792	chr6:142192725-142399251	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1019170	chr6:142234933-142397088	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv886731	chr6:142287143-142364628	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv464069	chr6:142322456-142407741	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv604794	chr6:142322456-142407741	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142310800-142334400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:142324600-142335000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:142329000-142332400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:142329000-142333400	Enhancers	Hela-S3	cervix
5	chr6:142329200-142331200	Enhancers	HMEC	breast
6	chr6:142329200-142331200	Enhancers	NHEK	skin
7	chr6:142329200-142331600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:142329400-142335000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:142329400-142335000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:142329800-142334400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:142330000-142335000	Enhancers	NH-A	brain
12	chr6:142330000-142335400	Enhancers	NHDF-Ad	bronchial
13	chr6:142330200-142333000	Enhancers	HSMMtube	muscle
14	chr6:142330200-142333200	Enhancers	HSMM	muscle
15	chr6:142330200-142335000	Enhancers	NHLF	lung
16	chr6:142330400-142331200	Enhancers	Fetal Heart	heart
17	chr6:142330400-142331400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:142330400-142331400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr6:142330400-142331600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:142330400-142331600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:142330400-142333200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:142330400-142335000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:142330400-142335000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr6:142330400-142335000	Enhancers	Osteobl	bone
25	chr6:142330600-142331200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:142330600-142334400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:142330800-142331200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:142330800-142331600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:142331000-142331600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr6:142331000-142331600	Enhancers	K562	blood
31	chr6:142331000-142333800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:142331000-142335000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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