Variant report

Variant	rs7172283
Chromosome Location	chr15:51369938-51369939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51369846..51371711-chr15:51377906..51380775,3	MCF-7	breast:
2	chr15:51365899..51367526-chr15:51369188..51370738,2	MCF-7	breast:
3	chr15:51369856..51370415-chr9:19379687..19380380,2	NB4	blood:
4	chr15:51368454..51371026-chr15:51376284..51379818,3	K562	blood:
5	chr15:51369526..51371616-chr15:51378318..51381028,2	K562	blood:
6	chr15:51200864..51202454-chr15:51366982..51369964,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137154	Chromatin interaction
ENSG00000081014	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11631783	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs11634895	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11639007	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11639350	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11853182	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854585	0.80[ASN][1000 genomes]
rs11856609	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12899586	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900916	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12911715	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16953046	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17522120	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs34590712	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34810611	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35684604	0.80[ASN][1000 genomes]
rs35827195	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3825799	0.86[YRI][hapmap]
rs7162562	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7170570	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8026140	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8034812	0.80[ASN][1000 genomes]
rs9652426	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv428634	chr15:51299632-51446666	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7172283	RP11-108K3.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51344600-51384400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:51366800-51370800	Enhancers	Spleen	Spleen
3	chr15:51367600-51371400	Weak transcription	HMEC	breast
4	chr15:51367600-51371600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:51367600-51372200	Weak transcription	NHEK	skin
6	chr15:51368200-51370600	Enhancers	K562	blood
7	chr15:51368600-51372000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:51368600-51372200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:51368600-51372600	Weak transcription	HSMM	muscle
10	chr15:51368800-51370400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr15:51368800-51370800	Enhancers	Stomach Mucosa	stomach
12	chr15:51369000-51370200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr15:51369000-51370400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:51369000-51370400	Enhancers	Fetal Heart	heart
15	chr15:51369000-51372200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr15:51369200-51370000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr15:51369200-51370000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:51369200-51370000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr15:51369200-51370200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr15:51369200-51370200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr15:51369200-51370800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:51369400-51370000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
23	chr15:51369400-51370000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr15:51369400-51370000	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr15:51369400-51370000	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr15:51369400-51370000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:51369400-51370000	Active TSS	Colonic Mucosa	Colon
28	chr15:51369400-51370000	Active TSS	Duodenum Mucosa	Duodenum
29	chr15:51369400-51370000	Active TSS	Fetal Brain Female	brain
30	chr15:51369400-51370000	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr15:51369400-51370200	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr15:51369400-51370200	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr15:51369400-51370200	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr15:51369400-51370200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:51369400-51370200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:51369400-51370200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:51369400-51370200	Active TSS	Brain Germinal Matrix	brain
38	chr15:51369400-51370200	Flanking Active TSS	Fetal Stomach	stomach
39	chr15:51369400-51370200	Flanking Active TSS	Fetal Thymus	thymus
40	chr15:51369400-51370400	Flanking Active TSS	GM12878-XiMat	blood
41	chr15:51369400-51370400	Flanking Active TSS	Osteobl	bone
42	chr15:51369400-51370800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:51369400-51377600	Weak transcription	Aorta	Aorta
44	chr15:51369600-51370000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr15:51369600-51370000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:51369600-51370000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr15:51369600-51370000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr15:51369600-51370000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:51369600-51370000	Active TSS	Primary T cells from cord blood	blood
50	chr15:51369600-51370000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood

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