Variant report

Variant	rs881844
Chromosome Location	chr17:37810218-37810219
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:175)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:175 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr17:37809828-37810497	K562	blood:	n/a	n/a
2	EP300	chr17:37809977-37810480	HepG2	liver:	n/a	n/a
3	RUNX3	chr17:37810116-37810466	GM12878	blood:	n/a	n/a
4	CTCF	chr17:37809995-37810742	HCT-116	colon:	n/a	n/a
5	EBF1	chr17:37810117-37810353	GM12878	blood:	n/a	n/a
6	CTCF	chr17:37810200-37810350	HA-sp	spinal cord:	n/a	n/a
7	CTCF	chr17:37810008-37810413	MCF-7	breast:	n/a	n/a
8	RAD21	chr17:37810108-37810419	Hela-S3	cervix:	n/a	chr17:37810379-37810389 chr17:37810377-37810389
9	CTCF	chr17:37810073-37810457	A549	lung:	n/a	n/a
10	RAD21	chr17:37810024-37810512	ECC-1	luminal epithelium:	n/a	chr17:37810088-37810098 chr17:37810379-37810389 chr17:37810377-37810389
11	CTCF	chr17:37810189-37810427	GM10266	blood:	n/a	n/a
12	CTCF	chr17:37810200-37810350	WERI-Rb-1	eye:	n/a	n/a
13	CTCF	chr17:37810200-37810350	GM12864	blood:	n/a	n/a
14	RAD21	chr17:37810146-37810451	A549	lung:	n/a	chr17:37810379-37810389 chr17:37810377-37810389
15	SIN3A	chr17:37810139-37810450	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr17:37810140-37810290	HFF-Myc	foreskin:	n/a	n/a
17	CTCF	chr17:37810157-37810430	MCF-7	breast:	n/a	n/a
18	TCF12	chr17:37809866-37810461	A549	lung:	n/a	n/a
19	MAZ	chr17:37810184-37810382	Hela-S3	cervix:	n/a	n/a
20	ZMIZ1	chr17:37810073-37810351	K562	blood:	n/a	n/a
21	MAZ	chr17:37810147-37810444	GM12878	blood:	n/a	n/a
22	CTCF	chr17:37810185-37810416	MCF-7	breast:	n/a	n/a
23	CTCF	chr17:37810180-37810330	HRE	kidney:	n/a	n/a
24	SMC3	chr17:37810108-37810471	HepG2	liver:	n/a	n/a
25	CTCF	chr17:37810093-37810446	HepG2	liver:	n/a	n/a
26	BHLHE40	chr17:37810161-37810433	GM12878	blood:	n/a	n/a
27	TBL1XR1	chr17:37810117-37810403	K562	blood:	n/a	n/a
28	CTCF	chr17:37810163-37810423	GM13976	blood:	n/a	n/a
29	TEAD4	chr17:37809865-37810477	HepG2	liver:	n/a	n/a
30	RAD21	chr17:37810112-37810444	IMR90	lung:	n/a	chr17:37810379-37810389 chr17:37810377-37810389
31	RCOR1	chr17:37809914-37810466	K562	blood:	n/a	n/a
32	CTCFL	chr17:37810159-37810390	K562	blood:	n/a	n/a
33	CTCF	chr17:37810057-37810519	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr17:37810200-37810350	BE2_C	brain:	n/a	n/a
35	JUND	chr17:37810040-37810416	HepG2	liver:	n/a	n/a
36	CTCF	chr17:37810200-37810350	AG04449	skin:	n/a	n/a
37	CTCF	chr17:37810200-37810350	GM12873	blood:	n/a	n/a
38	ZNF143	chr17:37810093-37810481	GM12878	blood:	n/a	n/a
39	UBTF	chr17:37810172-37810354	K562	blood:	n/a	n/a
40	CTCF	chr17:37810200-37810350	HAc	cerebellar:	n/a	n/a
41	CTCF	chr17:37810078-37810440	MCF-7	breast:	n/a	n/a
42	CTCF	chr17:37810152-37810384	A549	lung:	n/a	n/a
43	RAD21	chr17:37810186-37810378	GM12878	blood:	n/a	n/a
44	CTCF	chr17:37810140-37810467	NHEK	skin:	n/a	n/a
45	CTCF	chr17:37810174-37810445	Lung_OC	lung:	n/a	n/a
46	CTCF	chr17:37810146-37810465	K562	blood:	n/a	n/a
47	CTCF	chr17:37810166-37810422	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr17:37810200-37810350	GM12878	blood:	n/a	n/a
49	CTCF	chr17:37810055-37810472	H1-hESC	embryonic stem cell:	n/a	n/a
50	SMC3	chr17:37810115-37810453	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:37777903..37778847-chr17:37809797..37810807,7	K562	blood:
2	chr17:37810058..37810709-chr17:37910120..37910665,2	K562	blood:
3	chr17:37809503..37812375-chr17:37822536..37826640,4	K562	blood:
4	chr17:37789952..37790826-chr17:37809840..37810573,2	K562	blood:

No data

Variant related genes	Relation type
STARD3	TF binding region
ENSG00000141744	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1018246	0.91[ASN][1000 genomes]
rs1053651	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10852934	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11651497	0.87[ASN][1000 genomes]
rs11658786	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11869286	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12150298	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12150603	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs12453682	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs12940986	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs14050	0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1476278	0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1495099	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1495100	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1495101	0.91[ASN][1000 genomes]
rs1495102	0.91[ASN][1000 genomes]
rs1565920	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1565922	0.82[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1874228	0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1877031	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247862	0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2271308	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2271309	0.84[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2313171	0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2517952	0.82[ASN][1000 genomes]
rs2517953	0.86[ASN][1000 genomes]
rs2517954	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2517955	0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2517956	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2517957	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs2517958	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs2517959	0.85[ASN][1000 genomes]
rs2517960	0.83[ASN][1000 genomes]
rs2934951	0.91[ASN][1000 genomes]
rs2934952	0.91[ASN][1000 genomes]
rs2934953	0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2934956	0.91[ASN][1000 genomes]
rs2941503	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2941504	0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2941505	0.83[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2941506	0.81[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2952151	0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2952152	0.90[ASN][1000 genomes]
rs33953566	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35734596	0.82[ASN][1000 genomes]
rs3751903	0.87[ASN][1000 genomes]
rs3764351	0.84[EUR][1000 genomes]
rs3764352	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764353	0.87[ASN][1000 genomes]
rs3794712	0.83[ASN][1000 genomes]
rs3817160	0.87[ASN][1000 genomes]
rs407307	0.89[ASN][1000 genomes]
rs4794817	0.87[ASN][1000 genomes]
rs4795388	0.81[ASN][1000 genomes]
rs4795389	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4795390	0.87[ASN][1000 genomes]
rs732083	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs732084	0.91[ASN][1000 genomes]
rs8077172	0.91[ASN][1000 genomes]
rs8078228	0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs879606	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs903501	0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs903502	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs907087	0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs907088	0.91[ASN][1000 genomes]
rs907089	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs907090	0.91[ASN][1000 genomes]
rs907094	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9303274	0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs931992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9675194	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs9915323	0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs9972882	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv516757	chr17:37781849-37834541	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv908213	chr17:37807698-37839493	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs881844	PGAP3	cis	Muscle Skeletal	GTEx
rs881844	PGAP3	cis	Skin Sun Exposed Lower leg	GTEx
rs881844	PGAP3	cis	lung	GTEx
rs881844	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs881844	PGAP3	cis	Heart Left Ventricle	GTEx
rs881844	PGAP3	cis	Thyroid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37795000-37814000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr17:37795000-37823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:37795200-37814000	Weak transcription	Aorta	Aorta
4	chr17:37795200-37814600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr17:37795400-37818000	Weak transcription	Fetal Kidney	kidney
6	chr17:37796400-37810800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:37798200-37813800	Weak transcription	GM12878-XiMat	blood
8	chr17:37798800-37810400	Weak transcription	Fetal Thymus	thymus
9	chr17:37799800-37812400	Weak transcription	Psoas Muscle	Psoas
10	chr17:37799800-37819600	Weak transcription	Osteobl	bone
11	chr17:37800000-37812800	Weak transcription	NHLF	lung
12	chr17:37800000-37814000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr17:37800000-37815200	Weak transcription	HUVEC	blood vessel
14	chr17:37800000-37818600	Weak transcription	Hela-S3	cervix
15	chr17:37800000-37820000	Weak transcription	NH-A	brain
16	chr17:37800200-37810600	Enhancers	Fetal Brain Male	brain
17	chr17:37800200-37810600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr17:37800200-37816800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:37800400-37814000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:37800600-37816200	Weak transcription	NHEK	skin
21	chr17:37801000-37814600	Weak transcription	Primary B cells from cord blood	blood
22	chr17:37801800-37817000	Weak transcription	A549	lung
23	chr17:37803400-37814200	Strong transcription	Thymus	Thymus
24	chr17:37803800-37821800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:37804000-37812600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:37806800-37810800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr17:37807200-37810600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr17:37807200-37810600	Genic enhancers	Fetal Intestine Small	intestine
29	chr17:37807200-37810800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr17:37807200-37811000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr17:37807200-37811000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:37807200-37811200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:37807200-37811200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr17:37807400-37810400	Enhancers	Stomach Mucosa	stomach
35	chr17:37807400-37810600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr17:37807400-37811200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr17:37807800-37810600	Weak transcription	Primary T cells from cord blood	blood
38	chr17:37807800-37810800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr17:37807800-37811200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr17:37808000-37810600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr17:37808000-37810600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr17:37808000-37810600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:37808200-37810400	Enhancers	Brain Angular Gyrus	brain
44	chr17:37808200-37810600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:37808200-37811000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:37808200-37811000	Enhancers	Left Ventricle	heart
47	chr17:37808200-37812200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr17:37808400-37810400	Enhancers	Pancreas	Pancrea
49	chr17:37808400-37810400	Enhancers	Placenta Amnion	Placenta Amnion
50	chr17:37808400-37819200	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links