Variant report

Variant	rs2288934
Chromosome Location	chr19:39974103-39974104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39974055-39974117	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39973997-39974105	K562	blood:	n/a	n/a
4	POLR2A	chr19:39973155-39985792	PANC-1	pancreas:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39971121..39973511-chr19:39973741..39976891,3	MCF-7	breast:
2	chr19:39881392..39883533-chr19:39972449..39976025,3	K562	blood:
3	chr19:39973725..39975292-chr19:39977826..39980284,2	MCF-7	breast:
4	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:
5	chr19:39965047..39968880-chr19:39971509..39974367,5	MCF-7	breast:

No data

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000063322	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000105193	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10412931	0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs10423537	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10424217	0.88[EUR][1000 genomes]
rs1110627	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1130180	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12609112	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12978920	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12978954	0.83[EUR][1000 genomes]
rs12979605	0.82[EUR][1000 genomes]
rs12983040	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1529732	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1560730	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17626	0.82[CHB][hapmap]
rs1865091	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1865092	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1932	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2009970	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060270	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060271	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060272	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2116932	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2288933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304219	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304221	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353678	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2353679	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs251855	0.85[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs251856	0.87[EUR][1000 genomes]
rs251857	0.85[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs251858	0.88[EUR][1000 genomes]
rs251859	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs251860	0.84[EUR][1000 genomes]
rs28528765	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28620146	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28637729	0.86[EUR][1000 genomes]
rs28649498	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs31725	0.81[GIH][hapmap]
rs31727	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs31728	0.92[CEU][hapmap]
rs34918990	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35647910	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4390710	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802026	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803237	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803240	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803241	0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803242	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803247	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803250	0.89[EUR][1000 genomes]
rs481421	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs530411	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs564577	0.85[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs566130	0.85[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs59007555	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508862	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6508863	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508864	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508865	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs651601	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs686956	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7251384	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7251652	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7255253	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7257526	0.91[MEX][hapmap];0.88[TSI][hapmap]
rs73035416	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73549933	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8107194	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8107647	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8110134	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8110716	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8111260	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs878754	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2288934	MIR641	cis	lymphoblastoid	seeQTL
rs2288934	B3GNT8	cis	parietal	SCAN
rs2288934	GRIK5	cis	parietal	SCAN
rs2288934	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs2288934	BCAM	cis	parietal	SCAN
rs2288934	RPS16	cis	multi-tissue	Pritchard
rs2288934	RPS16	cis	Lymphoblastoid	GTEx
rs2288934	RPS16	cis	lymphoblastoid	seeQTL
rs2288934	NUMBL	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39972200-39986400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39972400-39976400	Weak transcription	Aorta	Aorta
3	chr19:39972600-39975000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:39972600-39975200	Weak transcription	Small Intestine	intestine
5	chr19:39972600-39976000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:39972600-39976200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:39972600-39976200	Weak transcription	Psoas Muscle	Psoas
8	chr19:39972600-39976400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:39972800-39974200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:39972800-39974200	Weak transcription	Left Ventricle	heart
11	chr19:39972800-39974200	Weak transcription	NH-A	brain
12	chr19:39972800-39974800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:39972800-39974800	Weak transcription	Osteobl	bone
14	chr19:39972800-39975200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:39972800-39975400	Weak transcription	Ovary	ovary
16	chr19:39972800-39975600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:39972800-39975800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr19:39972800-39975800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:39972800-39975800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:39972800-39975800	Weak transcription	Fetal Thymus	thymus
21	chr19:39972800-39976000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:39972800-39976000	Weak transcription	Esophagus	oesophagus
23	chr19:39972800-39976000	Weak transcription	HSMMtube	muscle
24	chr19:39972800-39976200	Weak transcription	Brain Substantia Nigra	brain
25	chr19:39972800-39976200	Weak transcription	Colonic Mucosa	Colon
26	chr19:39972800-39976200	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:39972800-39976200	Weak transcription	Pancreas	Pancrea
28	chr19:39972800-39976200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:39972800-39976200	Weak transcription	Right Ventricle	heart
30	chr19:39972800-39976400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:39972800-39976400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr19:39972800-39977000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr19:39972800-39977400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr19:39972800-39978800	Weak transcription	NHDF-Ad	bronchial
35	chr19:39972800-39980200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr19:39972800-39982200	Weak transcription	Fetal Kidney	kidney
37	chr19:39972800-39983200	Strong transcription	Fetal Brain Female	brain
38	chr19:39972800-39983600	Strong transcription	Fetal Stomach	stomach
39	chr19:39972800-39984200	Weak transcription	Stomach Mucosa	stomach
40	chr19:39972800-39988600	Weak transcription	Right Atrium	heart
41	chr19:39973000-39974200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:39973000-39974400	Weak transcription	Primary B cells from cord blood	blood
43	chr19:39973000-39974600	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:39973000-39975000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr19:39973000-39975400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr19:39973000-39975400	Weak transcription	HepG2	liver
47	chr19:39973000-39975800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:39973000-39976000	Weak transcription	Brain Hippocampus Middle	brain
49	chr19:39973000-39976000	Weak transcription	Hela-S3	cervix
50	chr19:39973000-39976200	Weak transcription	Duodenum Mucosa	Duodenum

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