Variant report

Variant	rs31727
Chromosome Location	chr19:39915637-39915638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39914133-39915704	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:39915367-39915760	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr19:39913199-39917525	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39915333-39916088	A549	lung:	n/a	n/a
5	POLR2A	chr19:39915619-39915882	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:39915119-39915717	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:39915446-39916179	A549	lung:	n/a	n/a
9	POLR2A	chr19:39915592-39916358	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr19:39914741-39916120	K562	blood:	n/a	n/a
11	JUND	chr19:39915383-39916041	A549	lung:	n/a	n/a
12	POLR2A	chr19:39915454-39915922	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:39915373-39916123	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:39915596-39916695	K562	blood:	n/a	n/a
15	POLR2A	chr19:39914610-39917398	GM12892	blood:	n/a	n/a
16	REST	chr19:39913175-39917362	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr19:39914765-39917562	K562	blood:	n/a	n/a
18	POLR2A	chr19:39915555-39916041	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr19:39915347-39916581	PFSK-1	brain:	n/a	n/a
21	CREB1	chr19:39915549-39915941	A549	lung:	n/a	n/a
22	EGR1	chr19:39915628-39915872	K562	blood:	n/a	n/a
23	SIN3AK20	chr19:39913141-39929158	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr19:39914764-39917848	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr19:39915260-39915722	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr19:39913839-39917581	GM12892	blood:	n/a	n/a
27	POLR2A	chr19:39914695-39917419	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:39913308-39917626	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39913480..39916274-chr19:39975273..39977291,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269410	TF binding region
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10412931	0.89[CEU][hapmap]
rs10423537	0.80[EUR][1000 genomes]
rs10424217	0.89[EUR][1000 genomes]
rs1110627	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs1130180	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12609112	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12978920	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12983040	0.83[AMR][1000 genomes]
rs1529732	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1560730	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17626	0.91[CHB][hapmap]
rs1865091	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1865092	0.92[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1932	0.92[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2009970	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2060270	0.85[AMR][1000 genomes]
rs2060271	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2116932	0.92[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2288933	0.92[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs2288934	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2304219	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs2304221	0.80[EUR][1000 genomes]
rs2353678	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2353679	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs251855	0.96[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs251856	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs251857	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs251858	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs251859	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs251860	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28528765	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28637729	0.80[AMR][1000 genomes]
rs28649498	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs31725	0.88[ASW][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs31726	0.94[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs31728	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34918990	0.81[EUR][1000 genomes]
rs4390710	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4802026	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803237	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4803240	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4803241	0.80[AMR][1000 genomes]
rs4803242	0.80[AMR][1000 genomes]
rs4803245	0.92[CEU][hapmap]
rs4803246	0.92[CEU][hapmap];0.84[GIH][hapmap]
rs4803247	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs481421	0.86[CHB][hapmap]
rs530411	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs564577	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs566130	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59007555	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6508862	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs651601	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs686956	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251652	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7255253	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73035416	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73549933	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8107194	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8107647	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8110134	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8110716	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs878754	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
3	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
5	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
7	nsv911688	chr19:39891219-39919538	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs31727	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs31727	RPS16	cis	lymphoblastoid	seeQTL
rs31727	NUMBL	cis	parietal	SCAN
rs31727	B3GNT8	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39904800-39921000	Weak transcription	Small Intestine	intestine
2	chr19:39904800-39925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39905000-39921200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:39905200-39916600	Weak transcription	Brain Hippocampus Middle	brain
5	chr19:39905200-39916600	Weak transcription	Brain Substantia Nigra	brain
6	chr19:39905200-39918800	Weak transcription	Pancreas	Pancrea
7	chr19:39905400-39916000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:39905400-39921200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:39905400-39921200	Weak transcription	K562	blood
10	chr19:39905400-39923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:39905600-39916400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:39905600-39921600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr19:39905800-39917000	Strong transcription	Thymus	Thymus
14	chr19:39905800-39918000	Weak transcription	HepG2	liver
15	chr19:39905800-39923000	Weak transcription	Brain Anterior Caudate	brain
16	chr19:39905800-39923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:39906200-39916000	Strong transcription	Fetal Intestine Small	intestine
18	chr19:39906200-39919000	Weak transcription	HMEC	breast
19	chr19:39906400-39916200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:39906400-39916800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:39906400-39917200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr19:39906400-39921200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:39906600-39916600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:39906600-39916600	Strong transcription	Fetal Thymus	thymus
25	chr19:39906600-39916800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr19:39906800-39916600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:39906800-39916600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:39906800-39916800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:39907000-39915800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:39907000-39916600	Strong transcription	Fetal Brain Female	brain
31	chr19:39907000-39917200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:39907000-39919000	Weak transcription	Right Atrium	heart
33	chr19:39907200-39916800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:39907200-39917200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:39907400-39916000	Strong transcription	NHLF	lung
36	chr19:39907400-39916200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr19:39907400-39916400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:39907600-39916000	Strong transcription	Right Ventricle	heart
39	chr19:39907600-39916400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr19:39907600-39916800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:39907600-39916800	Strong transcription	Brain Germinal Matrix	brain
42	chr19:39907600-39918200	Weak transcription	Fetal Heart	heart
43	chr19:39907800-39916200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:39907800-39917000	Strong transcription	Fetal Stomach	stomach
45	chr19:39907800-39918200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:39908000-39916800	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr19:39908000-39917200	Strong transcription	Primary T cells from cord blood	blood
48	chr19:39908400-39916400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr19:39908400-39916800	Strong transcription	Spleen	Spleen
50	chr19:39908400-39917200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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