Variant report

Variant	rs10948506
Chromosome Location	chr6:49465379-49465380
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr6:49464977-49465460	ECC-1	luminal epithelium:	n/a	chr6:49465247-49465262 chr6:49465213-49465225
2	NFIC	chr6:49464941-49465621	ECC-1	luminal epithelium:	n/a	n/a
3	FOXA1	chr6:49465046-49465385	ECC-1	luminal epithelium:	n/a	chr6:49465247-49465262 chr6:49465213-49465225
4	NFIC	chr6:49464954-49465529	ECC-1	luminal epithelium:	n/a	n/a
5	ESR1	chr6:49465026-49465421	ECC-1	luminal epithelium:	n/a	n/a
6	TEAD4	chr6:49464910-49465559	ECC-1	luminal epithelium:	n/a	n/a
7	FOXM1	chr6:49464868-49465588	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr6:49464896-49465604	ECC-1	luminal epithelium:	n/a	n/a
9	FOXA1	chr6:49465044-49465404	T-47D	breast:	n/a	chr6:49465247-49465262 chr6:49465213-49465225
10	TCF12	chr6:49464991-49465576	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr6:49464839-49465566	ECC-1	luminal epithelium:	n/a	n/a
12	TEAD4	chr6:49464942-49465471	ECC-1	luminal epithelium:	n/a	n/a
13	ESR1	chr6:49464987-49465434	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49460315..49462517-chr6:49463838..49466982,4	K562	blood:

Variant related genes	Relation type
GLYATL3	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10948505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948507	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189789	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12191171	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12197340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198507	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202875	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204398	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204617	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206768	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208117	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208221	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214010	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12214609	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17663557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17663627	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127756	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127759	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229385	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57912929	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6928563	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7755833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774623	0.86[EUR][1000 genomes];0.90[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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1019611	chr6:49431569-49470663	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1793167	chr6:49459978-49466686	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1799212	chr6:49459978-49466791	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49432600-49472000	Weak transcription	NHEK	skin
2	chr6:49451400-49467400	Weak transcription	Fetal Intestine Small	intestine
3	chr6:49458000-49466600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:49458400-49472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:49458600-49473800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:49460400-49473200	Weak transcription	HepG2	liver
7	chr6:49460600-49473600	Weak transcription	Stomach Mucosa	stomach
8	chr6:49461400-49472400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:49461600-49466800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:49461800-49467000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:49462200-49467000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:49465200-49465400	Enhancers	Fetal Brain Male	brain

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