Variant report

Variant	rs178791
Chromosome Location	chr17:16127206-16127207
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16118736..16121992-chr17:16123895..16128426,5	MCF-7	breast:
2	chr17:16118757..16122338-chr17:16126613..16132237,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108474	Chromatin interaction
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1029809	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs1065822	0.96[CEU][hapmap]
rs1075901	0.85[CEU][hapmap]
rs1079533	0.96[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs10852833	0.82[AMR][1000 genomes]
rs11078332	0.88[AMR][1000 genomes]
rs1125156	0.96[CEU][hapmap]
rs1126148	0.86[AMR][1000 genomes]
rs1160109	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes]
rs11650427	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs11650678	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs11651290	0.96[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs11653650	0.85[AFR][1000 genomes]
rs11655773	0.90[AMR][1000 genomes]
rs11657160	0.89[CEU][hapmap]
rs11872032	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs12150017	0.88[AMR][1000 genomes]
rs12936233	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12939418	0.80[AMR][1000 genomes]
rs12945855	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12947205	0.83[AMR][1000 genomes]
rs178657	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes]
rs178658	0.86[AMR][1000 genomes]
rs178659	0.92[AMR][1000 genomes]
rs178662	0.90[AMR][1000 genomes]
rs178789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178790	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178793	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178794	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs178795	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178796	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs178797	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178798	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]
rs178799	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178800	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs178801	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178802	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178804	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs178805	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178809	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs178814	0.89[CEU][hapmap]
rs178815	0.89[CEU][hapmap]
rs178816	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs178817	0.85[AMR][1000 genomes]
rs178820	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes]
rs178822	0.89[CEU][hapmap]
rs178829	0.88[AMR][1000 genomes]
rs178834	0.94[AMR][1000 genomes]
rs178837	0.89[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes]
rs178838	0.89[CEU][hapmap]
rs178839	0.89[CEU][hapmap]
rs1972503	0.92[AMR][1000 genomes]
rs1989856	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes]
rs2078050	0.89[CEU][hapmap]
rs2157990	0.85[CEU][hapmap]
rs2157991	0.89[CEU][hapmap]
rs2157992	0.96[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2301652	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs2324141	0.89[CEU][hapmap]
rs2324142	0.89[CEU][hapmap]
rs34351630	0.81[AMR][1000 genomes]
rs35160872	0.84[AMR][1000 genomes]
rs35799415	0.88[AMR][1000 genomes]
rs3785628	0.89[CEU][hapmap]
rs3785631	0.96[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs3815039	0.96[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs4435297	0.85[CEU][hapmap]
rs4791662	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes]
rs4792715	0.85[CEU][hapmap]
rs4792717	0.89[CEU][hapmap]
rs4792718	0.85[CEU][hapmap]
rs4792721	0.83[TSI][hapmap]
rs545738	0.87[AMR][1000 genomes]
rs6502488	0.89[CEU][hapmap]
rs7210990	0.82[YRI][hapmap]
rs7214695	0.89[CEU][hapmap]
rs7216834	0.92[AMR][1000 genomes]
rs7223346	0.89[CEU][hapmap]
rs8076864	0.96[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs8079969	0.89[CEU][hapmap]
rs8080706	0.82[AMR][1000 genomes]
rs9890012	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs9891379	0.96[CEU][hapmap];0.81[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs9891646	0.92[AMR][1000 genomes]
rs9902141	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes]
rs9903464	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes]
rs9907313	0.92[AMR][1000 genomes]
rs9908031	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs9909697	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9916220	0.86[AFR][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	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

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs178791	ADORA2B	cis	Esophagus Muscularis	GTEx
rs178791	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs178791	ADORA2B	cis	Artery Tibial	GTEx
rs178791	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs178791	ADORA2B	cis	Nerve Tibial	GTEx
rs178791	LOC125150	cis	normal skin	skin_eQTL
rs178791	CENPV	cis	Artery Tibial	GTEx
rs178791	NCOR1	cis	parietal	SCAN
rs178791	LOC125150	cis	uninvolved skin	skin_eQTL
rs178791	CENPV	cis	lymphoblastoid	seeQTL
rs178791	SREBF1	cis	cerebellum	SCAN
rs178791	ADORA2B	cis	Muscle Skeletal	GTEx
rs178791	LOC125150	cis	lesional skin	skin_eQTL
rs178791	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs178791	TTC19	cis	lymphoblastoid	seeQTL
rs178791	ZSWIM7	cis	Muscle Skeletal	GTEx
rs178791	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs178791	ADORA2B	cis	Thyroid	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16121000-16163200	Weak transcription	Spleen	Spleen
2	chr17:16121200-16131000	Weak transcription	Gastric	stomach
3	chr17:16121200-16141400	Weak transcription	Brain Substantia Nigra	brain
4	chr17:16121200-16142800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:16121200-16157000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:16121200-16158800	Weak transcription	Left Ventricle	heart
7	chr17:16121200-16159800	Weak transcription	Lung	lung
8	chr17:16121200-16163000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:16121400-16128600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr17:16121400-16129600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr17:16121400-16129600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr17:16121400-16129600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr17:16121400-16130000	Weak transcription	Right Ventricle	heart
14	chr17:16121400-16132200	Weak transcription	HSMM	muscle
15	chr17:16121400-16132200	Weak transcription	NHLF	lung
16	chr17:16121400-16133000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:16121400-16133200	Weak transcription	Fetal Thymus	thymus
18	chr17:16121400-16137400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr17:16121400-16140200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr17:16121400-16140400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr17:16121400-16141400	Weak transcription	Colon Smooth Muscle	Colon
22	chr17:16121400-16158600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr17:16121400-16158800	Weak transcription	Fetal Muscle Leg	muscle
24	chr17:16121400-16159000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr17:16121400-16170600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:16121600-16127600	Weak transcription	Brain Angular Gyrus	brain
27	chr17:16121600-16132000	Weak transcription	NHDF-Ad	bronchial
28	chr17:16121600-16132800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr17:16121600-16137000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr17:16121600-16137600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr17:16121600-16139200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr17:16121600-16139400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr17:16121600-16143000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:16121600-16143000	Weak transcription	Fetal Lung	lung
35	chr17:16121600-16147000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr17:16121600-16150200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr17:16121600-16151800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr17:16121600-16158400	Weak transcription	Brain Hippocampus Middle	brain
39	chr17:16121600-16158600	Weak transcription	Brain Germinal Matrix	brain
40	chr17:16121800-16129400	Weak transcription	Primary T cells from cord blood	blood
41	chr17:16121800-16132000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr17:16121800-16132600	Weak transcription	HUVEC	blood vessel
43	chr17:16121800-16132800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr17:16121800-16132800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr17:16121800-16132800	Weak transcription	NH-A	brain
46	chr17:16121800-16132800	Weak transcription	Osteobl	bone
47	chr17:16121800-16134000	Weak transcription	Fetal Intestine Large	intestine
48	chr17:16121800-16134200	Weak transcription	Fetal Kidney	kidney
49	chr17:16121800-16137000	Weak transcription	HMEC	breast
50	chr17:16121800-16139000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links