Variant report

Variant	rs12983263
Chromosome Location	chr19:18631631-18631632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:33)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18576760..18579549-chr19:18629981..18632725,2	K562	blood:
2	chr19:18629832..18635572-chr19:18680910..18686315,11	K562	blood:
3	chr19:18391161..18393749-chr19:18629899..18632279,2	K562	blood:
4	chr19:18630901..18633071-chr19:18792367..18795663,3	K562	blood:
5	chr19:18630460..18632741-chr19:18969591..18971985,2	K562	blood:
6	chr19:18630375..18633112-chr19:18747617..18750132,3	K562	blood:
7	chr19:18631013..18633168-chr19:18641014..18643926,2	MCF-7	breast:
8	chr19:18615204..18616917-chr19:18630702..18632857,2	MCF-7	breast:
9	chr19:18630875..18635401-chr19:18651200..18655863,9	MCF-7	breast:
10	chr19:18629748..18634724-chr19:18652806..18658264,15	K562	blood:
11	chr19:18612893..18615470-chr19:18630495..18632321,2	MCF-7	breast:
12	chr19:18630919..18637145-chr19:18698949..18704438,10	K562	blood:
13	chr19:18629832..18634516-chr19:18680910..18685097,11	K562	blood:
14	chr19:18629917..18634196-chr19:18652150..18655589,5	MCF-7	breast:
15	chr19:18527987..18529989-chr19:18630753..18632961,2	K562	blood:
16	chr19:18547268..18549412-chr19:18631404..18632910,2	K562	blood:
17	chr19:18629959..18634840-chr19:18652830..18656407,13	K562	blood:
18	chr19:18628801..18634367-chr19:18680492..18684131,12	MCF-7	breast:
19	chr19:18546603..18548898-chr19:18631485..18634393,2	MCF-7	breast:
20	chr19:18530114..18532262-chr19:18631255..18634040,2	MCF-7	breast:
21	chr19:18631032..18633728-chr19:18697675..18701681,7	MCF-7	breast:
22	chr19:18629894..18632720-chr19:18792259..18794365,2	K562	blood:
23	chr19:18631281..18633201-chr19:18647451..18649167,2	K562	blood:
24	chr19:18629458..18632220-chr19:18675761..18678411,2	K562	blood:
25	chr19:18630485..18634839-chr19:18666846..18671916,7	MCF-7	breast:
26	chr19:18629422..18634718-chr19:18699285..18702887,8	K562	blood:
27	chr19:18630548..18633267-chr19:18667345..18670044,3	K562	blood:
28	chr19:18631082..18632968-chr19:18642302..18645147,3	K562	blood:
29	chr19:18631468..18633224-chr19:18643647..18646289,2	K562	blood:
30	chr19:18630810..18631679-chr19:18701058..18701904,2	K562	blood:
31	chr19:18629876..18632922-chr19:18647804..18650314,4	MCF-7	breast:
32	chr19:18631459..18633367-chr19:18667345..18670376,4	K562	blood:
33	chr19:18631257..18635225-chr19:18680941..18684038,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105701	Chromatin interaction
ENSG00000269191	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000167487	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000005007	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000268938	Chromatin interaction
ENSG00000105655	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000105662	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10402322	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10409346	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10409408	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10410797	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10413922	0.85[EUR][1000 genomes]
rs10416993	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10418331	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10418554	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420384	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10423802	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10426768	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1045631	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11086110	0.84[EUR][1000 genomes]
rs11668704	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11670392	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11672385	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11879757	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12980726	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12982295	0.84[EUR][1000 genomes]
rs1469412	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1469413	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1971093	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2013069	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162797	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303692	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28534973	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2891676	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34213500	0.84[EUR][1000 genomes]
rs35004712	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35742476	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4006662	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4303657	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4580317	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808135	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808802	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808803	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808805	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808806	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808807	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808808	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808811	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808812	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808813	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55715336	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57923655	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6512268	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6512269	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6512270	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6512271	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7246788	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7247540	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7249760	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252130	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252185	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7255936	0.84[EUR][1000 genomes]
rs7256530	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7258891	0.84[EUR][1000 genomes]
rs7259135	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7507218	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8100343	0.84[EUR][1000 genomes]
rs8102717	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8104247	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106068	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8106332	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8111397	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8111582	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8111824	0.84[EUR][1000 genomes]
rs8112372	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8112859	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs888668	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs888669	0.91[EUR][1000 genomes];0.85[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	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
5	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv1055794	chr19:18611545-18676933	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
11	nsv911283	chr19:18626732-18689830	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12983263	SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12983263	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12983263	ENSG00000105656	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18630000-18633600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:18630200-18632400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr19:18630600-18632000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:18630600-18632600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr19:18630600-18632800	Active TSS	Aorta	Aorta
6	chr19:18630800-18631800	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr19:18630800-18632000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:18630800-18632000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr19:18630800-18632000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:18630800-18632000	Flanking Active TSS	Dnd41	blood
11	chr19:18630800-18632200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr19:18630800-18632200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:18630800-18632200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr19:18630800-18632200	Enhancers	Fetal Brain Male	brain
15	chr19:18630800-18632400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr19:18630800-18632400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:18630800-18632400	Flanking Active TSS	Fetal Muscle Trunk	muscle
18	chr19:18630800-18632800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:18630800-18633000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr19:18630800-18633800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr19:18630800-18633800	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr19:18631000-18631800	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr19:18631000-18632000	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr19:18631000-18632000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr19:18631000-18632000	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr19:18631000-18632200	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr19:18631000-18632200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:18631000-18632200	Flanking Active TSS	Fetal Brain Female	brain
29	chr19:18631000-18632200	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr19:18631000-18632200	Flanking Active TSS	Fetal Stomach	stomach
31	chr19:18631000-18632200	Flanking Active TSS	Fetal Thymus	thymus
32	chr19:18631000-18632400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr19:18631000-18632400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr19:18631000-18632800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:18631000-18633000	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr19:18631000-18633000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:18631000-18633000	Active TSS	Esophagus	oesophagus
38	chr19:18631000-18633000	Active TSS	Pancreas	Pancrea
39	chr19:18631000-18633000	Active TSS	Psoas Muscle	Psoas
40	chr19:18631000-18633200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:18631000-18633400	Active TSS	Ovary	ovary
42	chr19:18631000-18633600	Active TSS	H9 Cell Line	embryonic stem cell
43	chr19:18631000-18633800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:18631000-18634000	Active TSS	GM12878-XiMat	blood
45	chr19:18631200-18631800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:18631200-18631800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:18631200-18631800	Weak transcription	Fetal Heart	heart
48	chr19:18631200-18631800	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr19:18631200-18632200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:18631200-18632400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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