Variant report

Variant	rs2656957
Chromosome Location	chr5:89822221-89822222
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:89821851-89826472	K562	blood:	n/a	n/a
2	POLR2A	chr5:89821783-89823769	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:89822095-89826185	IMR90	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89777835..89781277-chr5:89821033..89823702,3	K562	blood:
2	chr5:89765101..89767054-chr5:89819920..89822582,2	K562	blood:
3	chr5:89821102..89822996-chr5:89857418..89859041,2	K562	blood:
4	chr5:89821999..89823611-chr5:89823888..89826662,2	MCF-7	breast:
5	chr5:89810981..89813583-chr5:89821226..89822873,2	MCF-7	breast:
6	chr5:89772669..89774767-chr5:89820227..89822408,2	K562	blood:
7	chr5:89821919..89824561-chr5:89840686..89844146,3	MCF-7	breast:
8	chr5:89818873..89823263-chr5:89823614..89827101,4	MCF-7	breast:

No data

Variant related genes	Relation type
GPR98	TF binding region
ENSG00000176018	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10069050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154568	0.89[EUR][1000 genomes]
rs154569	0.89[EUR][1000 genomes]
rs154570	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs154572	0.84[EUR][1000 genomes]
rs154573	0.85[EUR][1000 genomes]
rs1553545	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171790	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250377	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs257850	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257851	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27201	0.91[EUR][1000 genomes]
rs37238	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37239	0.83[EUR][1000 genomes]
rs37240	0.83[EUR][1000 genomes]
rs42467	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs43149	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511393	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs526806	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556894	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59159252	0.84[ASN][1000 genomes]
rs594990	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs599432	0.87[EUR][1000 genomes]
rs679568	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884154	0.81[EUR][1000 genomes]
rs810974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers 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	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2656957	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:89793800-89823400	Weak transcription	Hela-S3	cervix
4	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
5	chr5:89802600-89824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:89805600-89823200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:89809000-89824000	Weak transcription	Right Ventricle	heart
8	chr5:89809000-89824400	Weak transcription	Psoas Muscle	Psoas
9	chr5:89809200-89824600	Weak transcription	Spleen	Spleen
10	chr5:89810000-89822400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:89810400-89822800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:89810600-89824400	Weak transcription	Lung	lung
13	chr5:89810800-89824400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:89810800-89824400	Weak transcription	Esophagus	oesophagus
15	chr5:89811000-89824000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:89811000-89824400	Weak transcription	Pancreas	Pancrea
17	chr5:89812600-89822400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:89813000-89823400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:89813400-89822800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:89813400-89824200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:89813400-89824400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:89813600-89823400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:89814200-89822600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:89814600-89822400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:89814800-89824000	Weak transcription	HSMMtube	muscle
26	chr5:89814800-89824200	Weak transcription	Brain Germinal Matrix	brain
27	chr5:89815000-89823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:89815000-89824400	Weak transcription	Gastric	stomach
29	chr5:89815200-89822400	Weak transcription	NHEK	skin
30	chr5:89815200-89823000	Weak transcription	A549	lung
31	chr5:89815200-89823800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:89815200-89824400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:89815200-89824400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:89815200-89824400	Weak transcription	Brain Substantia Nigra	brain
35	chr5:89816200-89822800	Weak transcription	HMEC	breast
36	chr5:89816400-89822400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr5:89816400-89824200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:89816600-89824000	Weak transcription	Aorta	Aorta
39	chr5:89816600-89824200	Weak transcription	Fetal Brain Male	brain
40	chr5:89816600-89824200	Weak transcription	Ovary	ovary
41	chr5:89817400-89824000	Weak transcription	Fetal Kidney	kidney
42	chr5:89817600-89824200	Weak transcription	Fetal Muscle Leg	muscle
43	chr5:89817800-89822400	Strong transcription	HUVEC	blood vessel
44	chr5:89818000-89822600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:89818000-89824200	Weak transcription	Brain Hippocampus Middle	brain
46	chr5:89818200-89822400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:89818200-89823200	Weak transcription	NHLF	lung
48	chr5:89818200-89824200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr5:89818200-89824200	Weak transcription	Fetal Stomach	stomach
50	chr5:89818200-89824400	Weak transcription	Left Ventricle	heart

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