Variant report

Variant	rs285757
Chromosome Location	chr15:93179175-93179176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93147223..93149686-chr15:93178777..93181726,2	MCF-7	breast:
2	chr15:93177241..93179900-chr20:34540760..34543268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171222	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12443091	0.89[CEU][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs12593636	1.00[ASN][1000 genomes]
rs12908852	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs1496712	0.90[EUR][1000 genomes]
rs1496726	0.89[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs16947098	1.00[ASN][1000 genomes]
rs16947102	1.00[ASN][1000 genomes]
rs16974307	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs184048	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2254142	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453901	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs285754	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285758	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285766	0.90[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs285772	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366789	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373481	0.84[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs406032	0.86[EUR][1000 genomes]
rs413450	0.88[EUR][1000 genomes]
rs426221	1.00[ASN][1000 genomes]
rs434826	0.82[EUR][1000 genomes]
rs503112	0.88[EUR][1000 genomes]
rs6496969	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs7178546	0.91[EUR][1000 genomes]
rs72758232	1.00[ASN][1000 genomes]
rs72758234	1.00[ASN][1000 genomes]
rs72758301	1.00[ASN][1000 genomes]
rs73454725	1.00[ASN][1000 genomes]
rs73454730	1.00[ASN][1000 genomes]
rs893379	0.89[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]

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	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	esv1808537	chr15:93146057-93191935	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv974717	chr15:93170490-93180185	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HIV-1 susceptibility	21160409	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs285757	PRC1	cis	parietal	SCAN
rs285757	RGMA	cis	parietal	SCAN
rs285757	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93163600-93180600	Weak transcription	Small Intestine	intestine
2	chr15:93167800-93179800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:93168200-93179800	Weak transcription	Spleen	Spleen
4	chr15:93168200-93180200	Weak transcription	Psoas Muscle	Psoas
5	chr15:93168400-93179200	Weak transcription	Adipose Nuclei	Adipose
6	chr15:93169000-93180400	Weak transcription	Fetal Kidney	kidney
7	chr15:93169200-93179200	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:93169200-93180200	Weak transcription	A549	lung
9	chr15:93170000-93180400	Weak transcription	HSMM	muscle
10	chr15:93171000-93197400	Weak transcription	Primary T cells from cord blood	blood
11	chr15:93171400-93180200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr15:93173600-93179600	Weak transcription	Ovary	ovary
13	chr15:93173600-93179800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:93173600-93180200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:93173800-93179600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:93173800-93179800	Weak transcription	Esophagus	oesophagus
17	chr15:93173800-93179800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr15:93173800-93180400	Weak transcription	Fetal Intestine Large	intestine
19	chr15:93173800-93180400	Weak transcription	Fetal Intestine Small	intestine
20	chr15:93176000-93182000	Enhancers	Pancreas	Pancrea
21	chr15:93176000-93182200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:93176200-93179800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:93176200-93180400	Enhancers	Stomach Mucosa	stomach
24	chr15:93176400-93180200	Enhancers	Fetal Heart	heart
25	chr15:93176800-93182600	Enhancers	Gastric	stomach
26	chr15:93177000-93180200	Enhancers	Stomach Smooth Muscle	stomach
27	chr15:93177000-93182600	Enhancers	Fetal Muscle Leg	muscle
28	chr15:93177200-93179800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:93177200-93180000	Enhancers	Fetal Stomach	stomach
30	chr15:93177200-93183000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr15:93177400-93179200	Enhancers	Brain Angular Gyrus	brain
32	chr15:93177400-93179200	Weak transcription	GM12878-XiMat	blood
33	chr15:93177400-93182400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr15:93177600-93179200	Enhancers	Brain Hippocampus Middle	brain
35	chr15:93177600-93179200	Weak transcription	Left Ventricle	heart
36	chr15:93177600-93179400	Enhancers	Brain Cingulate Gyrus	brain
37	chr15:93177600-93180400	Weak transcription	HSMMtube	muscle
38	chr15:93177600-93181200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr15:93177600-93182600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:93177800-93179200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:93177800-93181200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:93178000-93179400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr15:93178000-93179800	Weak transcription	Right Ventricle	heart
44	chr15:93178000-93180600	Enhancers	H9 Cell Line	embryonic stem cell
45	chr15:93178000-93181200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr15:93178000-93188400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr15:93178200-93182400	Enhancers	Fetal Lung	lung
48	chr15:93178400-93179600	Weak transcription	Right Atrium	heart
49	chr15:93178400-93179800	Weak transcription	Lung	lung
50	chr15:93178400-93180400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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