Variant report

Variant	rs7177248
Chromosome Location	chr15:52464373-52464374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52464249..52467192-chr15:52469129..52471507,3	K562	blood:
2	chr15:52462256..52465166-chr15:52466100..52468864,2	MCF-7	breast:
3	chr15:52463801..52465460-chr21:45777828..45779686,2	MCF-7	breast:
4	chr15:52462679..52469948-chr15:52470344..52473249,9	MCF-7	breast:
5	chr15:52447415..52450073-chr15:52464203..52465781,2	MCF-7	breast:
6	chr15:52388135..52390483-chr15:52464352..52466647,2	MCF-7	breast:
7	chr15:52463285..52465150-chr15:52473016..52475731,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12438169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12438190	0.84[ASN][1000 genomes]
rs12438194	0.92[CHB][hapmap]
rs12438274	0.85[ASN][1000 genomes]
rs12438743	0.91[CHB][hapmap]
rs12438937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12440354	0.93[ASN][1000 genomes]
rs12441074	0.93[ASN][1000 genomes]
rs12593041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12594679	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12594809	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12595160	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs12898389	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12899030	0.92[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12899343	0.92[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12901730	0.91[CHB][hapmap]
rs12901891	0.91[CHB][hapmap]
rs12902522	0.93[ASN][1000 genomes]
rs12904880	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12905698	0.91[ASN][1000 genomes]
rs12907835	0.83[CHB][hapmap]
rs12909161	0.82[CHB][hapmap]
rs12909184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12910052	0.91[ASN][1000 genomes]
rs12910398	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12910870	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916557	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2398	0.82[CHB][hapmap]
rs2414130	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2414132	0.84[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs34283892	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35709612	0.93[ASN][1000 genomes]
rs35733550	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35914910	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3794543	0.91[CHB][hapmap]
rs4238384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4506834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4638520	0.92[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4776007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4776008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776012	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62014721	0.92[ASN][1000 genomes]
rs62014722	0.91[ASN][1000 genomes]
rs7166799	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];0.99[ASN][1000 genomes]
rs7181580	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8026828	0.82[EUR][1000 genomes]
rs8029782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034097	0.83[CHB][hapmap]

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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7177248	BCL2L10	Cis_1M	lymphoblastoid	RTeQTL
rs7177248	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
2	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:52442600-52470400	Weak transcription	HMEC	breast
7	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:52445600-52471000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:52447400-52471000	Weak transcription	Right Atrium	heart
10	chr15:52448800-52465200	Weak transcription	Liver	Liver
11	chr15:52454200-52468200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:52455600-52470800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:52455800-52467800	Weak transcription	Thymus	Thymus
14	chr15:52455800-52468400	Weak transcription	Hela-S3	cervix
15	chr15:52455800-52471000	Weak transcription	Aorta	Aorta
16	chr15:52455800-52471000	Weak transcription	Gastric	stomach
17	chr15:52456000-52464800	Weak transcription	Pancreas	Pancrea
18	chr15:52456000-52468400	Weak transcription	Ovary	ovary
19	chr15:52456000-52470000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:52456000-52470600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:52456000-52470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:52456000-52471000	Weak transcription	HSMMtube	muscle
23	chr15:52456200-52467200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:52456200-52468200	Weak transcription	Fetal Brain Female	brain
25	chr15:52456200-52468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:52456200-52470200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:52456200-52470800	Weak transcription	Fetal Stomach	stomach
28	chr15:52456200-52470800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:52456200-52471000	Weak transcription	Spleen	Spleen
30	chr15:52462200-52464400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr15:52462600-52464400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:52462600-52464400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr15:52462600-52464400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr15:52462800-52464400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr15:52463000-52464400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr15:52463200-52464400	Enhancers	Primary T cells from cord blood	blood
37	chr15:52463200-52464400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr15:52463200-52464800	Enhancers	Primary B cells from peripheral blood	blood
39	chr15:52463200-52470600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:52463400-52464400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:52463400-52464400	Enhancers	Brain Angular Gyrus	brain
42	chr15:52463600-52464400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:52463600-52464400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr15:52463600-52464400	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr15:52463600-52468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:52463600-52470400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:52463800-52466600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr15:52463800-52470600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:52464000-52464400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:52464000-52464600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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