Variant report

Variant	rs16973089
Chromosome Location	chr15:42631171-42631172
allele	A/G
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	POLR2A	chr15:42631105-42631305	K562	blood:	n/a	n/a

Variant related genes	Relation type
GANC	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10518763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518766	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1060291	1.00[JPT][hapmap]
rs11022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11636577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1659215	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1679008	1.00[CEU][hapmap]
rs16973053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1712391	1.00[CEU][hapmap]
rs1712407	1.00[CEU][hapmap]
rs17695121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17766532	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1801449	0.82[CEU][hapmap]
rs1801496	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1900921	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412706	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412707	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364344	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364345	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364348	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364352	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364354	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364356	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364357	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364358	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364360	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364371	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364372	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899051	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34684858	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35039186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36023127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4453448	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583208	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs4923948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs598441	1.00[CEU][hapmap]
rs609660	1.00[CEU][hapmap]
rs613131	1.00[CEU][hapmap]
rs633483	1.00[CEU][hapmap]
rs635617	1.00[CEU][hapmap]
rs635919	1.00[CEU][hapmap]
rs663454	1.00[CEU][hapmap]
rs685521	1.00[CEU][hapmap]
rs7164437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166240	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170744	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728509	1.00[YRI][hapmap]
rs7497367	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026890	1.00[YRI][hapmap]
rs8033412	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8035332	1.00[YRI][hapmap]
rs8035521	1.00[YRI][hapmap]
rs8037100	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8037797	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038467	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042666	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9972331	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS 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 miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16973089	LRRC57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42568400-42656000	Weak transcription	Small Intestine	intestine
2	chr15:42573400-42635800	Weak transcription	Gastric	stomach
3	chr15:42601200-42636000	Weak transcription	Brain Germinal Matrix	brain
4	chr15:42603200-42636000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:42603400-42648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:42603400-42648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:42604000-42639400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:42604600-42651200	Weak transcription	Fetal Kidney	kidney
9	chr15:42606200-42634600	Weak transcription	Pancreas	Pancrea
10	chr15:42615600-42631800	Weak transcription	Lung	lung
11	chr15:42616200-42634600	Weak transcription	Fetal Stomach	stomach
12	chr15:42616200-42636600	Weak transcription	NHEK	skin
13	chr15:42616800-42636000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:42617000-42645000	Weak transcription	NHLF	lung
15	chr15:42618000-42636000	Weak transcription	Colonic Mucosa	Colon
16	chr15:42618600-42634800	Weak transcription	Placenta	Placenta
17	chr15:42619600-42634400	Weak transcription	Aorta	Aorta
18	chr15:42619600-42634400	Weak transcription	Ovary	ovary
19	chr15:42619600-42634800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:42619600-42635000	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:42619600-42635600	Weak transcription	Thymus	Thymus
22	chr15:42619600-42635600	Weak transcription	Spleen	Spleen
23	chr15:42619600-42640000	Weak transcription	NHDF-Ad	bronchial
24	chr15:42619600-42647200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:42619600-42656200	Weak transcription	HMEC	breast
26	chr15:42620200-42635000	Weak transcription	Brain Substantia Nigra	brain
27	chr15:42620600-42634600	Weak transcription	Fetal Intestine Large	intestine
28	chr15:42620600-42634800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:42621800-42635000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:42621800-42635800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:42621800-42636000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:42623800-42634800	Weak transcription	Brain Angular Gyrus	brain
33	chr15:42623800-42634800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:42623800-42635400	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:42623800-42635800	Weak transcription	Esophagus	oesophagus
36	chr15:42624000-42635600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:42626800-42643400	Weak transcription	Fetal Thymus	thymus
38	chr15:42627600-42634600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:42627600-42634600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:42627600-42634600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:42627600-42635400	Weak transcription	Left Ventricle	heart
42	chr15:42627600-42654600	Weak transcription	HSMM	muscle
43	chr15:42627800-42631600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr15:42627800-42634600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:42627800-42634600	Weak transcription	Psoas Muscle	Psoas
46	chr15:42627800-42634600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:42627800-42634800	Weak transcription	Adipose Nuclei	Adipose
48	chr15:42627800-42635000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:42627800-42635200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:42627800-42636600	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links