Variant report

Variant	rs4638520
Chromosome Location	chr15:52412103-52412104
allele	C/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	POLR2A	chr15:52411961-52412168	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52272323..52273861-chr15:52410160..52412706,2	MCF-7	breast:
2	chr15:52393195..52395806-chr15:52409581..52412180,2	K562	blood:
3	chr15:52309129..52311791-chr15:52409985..52412666,2	MCF-7	breast:
4	chr15:52264304..52267297-chr15:52410135..52412517,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259709	TF binding region
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12438169	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12438190	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12438194	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12438274	0.88[ASN][1000 genomes]
rs12438743	0.91[CEU][hapmap];0.96[GIH][hapmap]
rs12438937	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12440354	0.95[ASN][1000 genomes]
rs12440956	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12441074	0.95[ASN][1000 genomes]
rs12593041	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12899030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12899343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12901354	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12901730	0.91[CEU][hapmap]
rs12901891	0.91[CEU][hapmap]
rs12902073	1.00[CEU][hapmap]
rs12902522	1.00[CEU][hapmap];0.95[ASN][1000 genomes]
rs12904831	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12904889	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12905698	0.93[ASN][1000 genomes]
rs12907835	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12909161	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12909184	0.91[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs12910052	0.93[ASN][1000 genomes]
rs12910398	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12910870	0.90[ASN][1000 genomes]
rs12912428	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2398	0.86[CHB][hapmap];0.93[GIH][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2414130	0.93[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2414132	0.93[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35709612	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35733550	0.90[ASN][1000 genomes]
rs3794540	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3794543	1.00[CEU][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4238384	0.93[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs4506834	0.90[ASN][1000 genomes]
rs4636859	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4774608	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4776003	0.93[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes]
rs4776007	0.91[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs4776008	0.90[ASN][1000 genomes]
rs62014721	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62014722	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166799	0.93[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7177248	0.92[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs8029782	0.89[ASN][1000 genomes]
rs8034097	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4638520	ARPP19	cis	parietal	SCAN
rs4638520	GNB5	Cis_1M	lymphoblastoid	RTeQTL
rs4638520	KIAA1370	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52404800-52416400	Weak transcription	Aorta	Aorta
2	chr15:52404800-52428000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr15:52405000-52413200	Weak transcription	Primary T cells from cord blood	blood
4	chr15:52405000-52414800	Weak transcription	Primary B cells from cord blood	blood
5	chr15:52405000-52416400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:52405000-52416400	Weak transcription	Gastric	stomach
7	chr15:52405000-52416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr15:52405000-52416600	Weak transcription	Esophagus	oesophagus
9	chr15:52405000-52420400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:52405000-52421800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:52405000-52427400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:52405000-52427800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:52405000-52428800	Weak transcription	Fetal Heart	heart
14	chr15:52405200-52412400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:52405400-52426000	Weak transcription	Spleen	Spleen
16	chr15:52405600-52412800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:52406000-52412400	Weak transcription	Thymus	Thymus
18	chr15:52406000-52414200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:52406400-52427800	Weak transcription	Fetal Brain Male	brain
20	chr15:52407000-52412200	Weak transcription	Fetal Brain Female	brain
21	chr15:52407200-52416400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:52407400-52427600	Weak transcription	HSMMtube	muscle
23	chr15:52407600-52417800	Weak transcription	Brain Anterior Caudate	brain
24	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
25	chr15:52407800-52416800	Weak transcription	Brain Angular Gyrus	brain
26	chr15:52407800-52428800	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
28	chr15:52408000-52416200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:52408000-52416600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:52408200-52416400	Weak transcription	NHDF-Ad	bronchial
31	chr15:52408200-52425800	Weak transcription	Small Intestine	intestine
32	chr15:52408400-52414200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr15:52408600-52416400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:52408600-52425600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr15:52408800-52414000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:52408800-52428000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr15:52409000-52413200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:52409000-52414200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:52409000-52414200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:52409000-52416200	Weak transcription	HUVEC	blood vessel
41	chr15:52409000-52416400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:52409000-52416400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:52409000-52416400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:52409000-52416400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:52409000-52416400	Weak transcription	A549	lung
46	chr15:52409000-52416400	Weak transcription	K562	blood
47	chr15:52409000-52417000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:52409000-52418000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:52409000-52423400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:52409000-52426800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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