Variant report

Variant	rs16972770
Chromosome Location	chr15:42443526-42443527
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42430104..42432134-chr15:42441613..42443649,2	K562	blood:
2	chr15:42441690..42443791-chr15:42450046..42452930,3	K562	blood:
3	chr15:42438588..42441073-chr15:42442171..42444536,4	MCF-7	breast:
4	chr15:42442020..42443791-chr15:42450046..42452930,2	K562	blood:
5	chr15:42443129..42444925-chr15:42485873..42487790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168907	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10220859	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs12440087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs12441642	0.86[CHB][hapmap]
rs1624183	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1659213	1.00[CEU][hapmap]
rs1659218	1.00[CEU][hapmap]
rs1659219	1.00[CEU][hapmap]
rs1659222	1.00[CEU][hapmap]
rs1678992	1.00[CEU][hapmap]
rs16972776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972779	1.00[CHB][hapmap]
rs16972887	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16973008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs16973045	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16973060	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1703754	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2138831	0.85[CHB][hapmap]
rs2412688	1.00[CHB][hapmap]
rs2620386	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2918460	1.00[CEU][hapmap]
rs4506867	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4923932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4923945	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4924627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs4924672	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4924673	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs56670003	0.83[AMR][1000 genomes]
rs58292736	0.83[AMR][1000 genomes]
rs59138723	0.84[AMR][1000 genomes]
rs59974698	0.81[AMR][1000 genomes]
rs60486546	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60506946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs622714	0.93[EUR][1000 genomes]
rs624841	0.93[EUR][1000 genomes]
rs678778	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs681029	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7181979	0.80[AMR][1000 genomes]
rs73398938	0.83[AMR][1000 genomes]
rs73403545	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73403546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73403548	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403550	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407403	0.81[AMR][1000 genomes]
rs73407407	0.80[AMR][1000 genomes]
rs74009020	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025601	0.86[CHB][hapmap]

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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv9245	chr15:42441849-42453572	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42411600-42444200	Weak transcription	Right Atrium	heart
2	chr15:42435800-42443600	Weak transcription	Colonic Mucosa	Colon
3	chr15:42436000-42452000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:42439400-42443600	Weak transcription	Placenta	Placenta
5	chr15:42439400-42451200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:42439400-42451800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:42439600-42444200	Weak transcription	Fetal Intestine Small	intestine
8	chr15:42439600-42448600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr15:42441200-42450600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:42441600-42443600	Weak transcription	Left Ventricle	heart
11	chr15:42441600-42446200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:42441800-42451000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr15:42442000-42443600	Weak transcription	Fetal Heart	heart
14	chr15:42442600-42445000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:42442600-42447000	Enhancers	Esophagus	oesophagus
16	chr15:42442600-42447400	Weak transcription	Spleen	Spleen
17	chr15:42442800-42443800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:42442800-42445000	Enhancers	NHEK	skin
19	chr15:42442800-42445400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:42443000-42445000	Enhancers	Right Ventricle	heart
21	chr15:42443000-42445600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:42443200-42444200	Weak transcription	HMEC	breast
23	chr15:42443200-42445000	Enhancers	Brain Anterior Caudate	brain
24	chr15:42443400-42443800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:42443400-42444000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr15:42443400-42444800	Enhancers	Osteobl	bone
27	chr15:42443400-42445200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:42443400-42445400	Enhancers	Fetal Muscle Trunk	muscle
29	chr15:42443400-42447600	Enhancers	Gastric	stomach

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