Variant report

Variant	rs178798
Chromosome Location	chr17:16117359-16117360
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr17:16117097-16119798	SK-N-SH	brain:	n/a	n/a
2	RUNX3	chr17:16117219-16117637	GM12878	blood:	n/a	chr17:16117417-16117426

No.	Distal block	Cell Line	Cell type
1	chr17:16116365..16119285-chr17:16395133..16397532,2	K562	blood:
2	chr17:16115684..16120775-chr17:16282002..16285784,4	MCF-7	breast:
3	chr17:15901763..15905062-chr17:16117309..16121912,5	MCF-7	breast:
4	chr17:15902955..15905510-chr17:16117213..16119076,2	K562	blood:

Variant related genes	Relation type
PIGL	TF binding region
ENSG00000214941	Chromatin interaction
ENSG00000170315	Chromatin interaction
ENSG00000181350	Chromatin interaction
ENSG00000011295	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1029809	0.85[CEU][hapmap];0.85[CHB][hapmap];0.80[LWK][hapmap]
rs1065822	1.00[CEU][hapmap]
rs1075901	0.81[CEU][hapmap]
rs1079533	1.00[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs10852833	0.83[AMR][1000 genomes]
rs11078332	0.89[AMR][1000 genomes]
rs1125156	1.00[CEU][hapmap]
rs1126148	0.87[AMR][1000 genomes]
rs1160109	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs11650427	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs11650678	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs11651290	1.00[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs11655773	0.91[AMR][1000 genomes]
rs11657160	0.85[CEU][hapmap]
rs11869450	0.82[CEU][hapmap]
rs11872032	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs12150017	0.89[AMR][1000 genomes]
rs12936233	0.81[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12939418	0.81[AMR][1000 genomes]
rs12945855	0.81[CEU][hapmap];0.85[CHB][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12947205	0.84[AMR][1000 genomes]
rs178657	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs178658	0.87[AMR][1000 genomes]
rs178659	0.93[AMR][1000 genomes]
rs178662	0.91[AMR][1000 genomes]
rs178789	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178790	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178791	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178792	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178793	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178794	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178795	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178796	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs178797	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs178799	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178800	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs178801	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs178802	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs178804	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs178805	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs178806	0.85[ASN][1000 genomes]
rs178809	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs178814	0.85[CEU][hapmap]
rs178815	0.85[CEU][hapmap]
rs178816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs178817	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs178820	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs178822	0.85[CEU][hapmap]
rs178829	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs178830	0.80[AMR][1000 genomes]
rs178834	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs178837	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes]
rs178838	0.85[CEU][hapmap]
rs178839	0.85[CEU][hapmap]
rs1972503	0.93[AMR][1000 genomes]
rs1989856	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs2078050	0.85[CEU][hapmap]
rs2157990	0.81[CEU][hapmap]
rs2157991	0.85[CEU][hapmap]
rs2157992	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2301652	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs2324141	0.85[CEU][hapmap]
rs2324142	0.85[CEU][hapmap]
rs34351630	0.82[AMR][1000 genomes]
rs35160872	0.85[AMR][1000 genomes]
rs35799415	0.89[AMR][1000 genomes]
rs3785628	0.85[CEU][hapmap]
rs3785631	1.00[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs3785633	1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs3815039	1.00[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs4435297	0.81[CEU][hapmap]
rs4791662	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs4792715	0.82[CEU][hapmap]
rs4792717	0.85[CEU][hapmap]
rs4792718	0.82[CEU][hapmap]
rs4792721	0.83[TSI][hapmap]
rs545738	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6416868	0.85[CEU][hapmap]
rs6502488	0.85[CEU][hapmap]
rs7207889	0.81[AMR][1000 genomes]
rs7214695	0.85[CEU][hapmap]
rs7216834	0.93[AMR][1000 genomes]
rs7223346	0.85[CEU][hapmap]
rs8076864	1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs8079969	0.85[CEU][hapmap]
rs8080706	0.83[AMR][1000 genomes]
rs9890012	1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs9891379	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]
rs9891646	0.93[AMR][1000 genomes]
rs9899002	1.00[CEU][hapmap]
rs9902141	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs9903464	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes]
rs9907313	0.93[AMR][1000 genomes]
rs9908031	1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs9909697	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]

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	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv522169	chr17:15923709-16147821	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv907713	chr17:15981874-16127206	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv907715	chr17:16019978-16206540	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
8	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
9	nsv907718	chr17:16080849-16143709	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	nsv528263	chr17:16097430-16196996	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
11	nsv112235	chr17:16116824-16120100	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs178798	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs178798	ADORA2B	cis	Nerve Tibial	GTEx
rs178798	CENPV	cis	parietal	SCAN
rs178798	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs178798	LOC125150	cis	normal skin	skin_eQTL
rs178798	LOC125150	cis	lesional skin	skin_eQTL
rs178798	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs178798	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs178798	ADORA2B	cis	Muscle Skeletal	GTEx
rs178798	ADORA2B	cis	lung	GTEx
rs178798	CENPV	cis	Artery Tibial	GTEx
rs178798	TTC19	cis	lymphoblastoid	seeQTL
rs178798	LOC125150	cis	uninvolved skin	skin_eQTL
rs178798	ADORA2B	cis	Artery Tibial	GTEx
rs178798	NCOR1	cis	parietal	SCAN
rs178798	ZSWIM7	cis	Muscle Skeletal	GTEx
rs178798	ADORA2B	cis	Esophagus Muscularis	GTEx
rs178798	ADORA2B	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16105400-16118000	Weak transcription	Spleen	Spleen
2	chr17:16106800-16118000	Weak transcription	Lung	lung
3	chr17:16108400-16117600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:16108800-16117600	Weak transcription	Gastric	stomach
5	chr17:16112200-16117600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:16114000-16117400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr17:16114000-16117600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:16114800-16117400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr17:16114800-16119400	Active TSS	GM12878-XiMat	blood
10	chr17:16115000-16117400	Enhancers	Fetal Brain Male	brain
11	chr17:16115200-16117600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:16115400-16117600	Enhancers	Primary B cells from peripheral blood	blood
13	chr17:16115800-16117400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr17:16116000-16117600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr17:16116000-16117800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr17:16116200-16117400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr17:16116200-16117400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:16116200-16117400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr17:16116200-16117400	Enhancers	Brain Germinal Matrix	brain
20	chr17:16116200-16117400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr17:16116200-16117400	Weak transcription	Fetal Thymus	thymus
22	chr17:16116200-16117600	Enhancers	Colon Smooth Muscle	Colon
23	chr17:16116200-16119400	Active TSS	HepG2	liver
24	chr17:16116400-16117400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:16116400-16117400	Weak transcription	Ovary	ovary
26	chr17:16116400-16117600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:16116400-16117600	Weak transcription	Left Ventricle	heart
28	chr17:16116400-16118000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr17:16116400-16119200	Active TSS	Fetal Intestine Small	intestine
30	chr17:16116400-16119400	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr17:16116600-16117600	Weak transcription	Pancreas	Pancrea
32	chr17:16116600-16121400	Active TSS	Psoas Muscle	Psoas
33	chr17:16116800-16117400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:16116800-16117400	Enhancers	Primary hematopoietic stem cells	blood
35	chr17:16116800-16117600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr17:16116800-16117600	Enhancers	Brain Substantia Nigra	brain
37	chr17:16116800-16117600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr17:16116800-16117600	Enhancers	Placenta	Placenta
39	chr17:16116800-16117800	Flanking Active TSS	Dnd41	blood
40	chr17:16116800-16118000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr17:16116800-16118000	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr17:16116800-16118200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr17:16116800-16118200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:16116800-16118200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr17:16116800-16118200	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr17:16116800-16118200	Flanking Active TSS	Liver	Liver
47	chr17:16116800-16118800	Active TSS	Right Atrium	heart
48	chr17:16116800-16119000	Active TSS	Colonic Mucosa	Colon
49	chr17:16116800-16119200	Active TSS	NHLF	lung
50	chr17:16116800-16119400	Active TSS	H1 Cell Line	embryonic stem cell

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