Variant report

Variant	rs12947506
Chromosome Location	chr17:37707592-37707593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37707289..37708873-chr17:38136097..38138818,2	K562	blood:
2	chr17:37707435..37710259-chr17:37711841..37713472,2	K562	blood:
3	chr17:37694512..37696186-chr17:37706631..37708781,2	K562	blood:
4	chr17:37706585..37709656-chr17:37773837..37776005,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDK12-1	chr17:37707291-37707748	NONHSAT053446

Variant related genes	Relation type
ENSG00000214546	Chromatin interaction
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10445306	0.87[CHB][hapmap]
rs10491128	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs1054488	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10775391	0.83[ASN][1000 genomes]
rs1077715	0.83[ASN][1000 genomes]
rs10852933	0.85[ASN][1000 genomes]
rs10852934	0.83[CEU][hapmap]
rs11078898	0.82[CHB][hapmap]
rs11078901	0.82[CHB][hapmap]
rs11078902	0.82[CHB][hapmap]
rs11078906	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs11078907	0.80[CHB][hapmap]
rs11078910	0.81[ASN][1000 genomes]
rs11078911	0.81[ASN][1000 genomes]
rs11078912	0.81[ASN][1000 genomes]
rs11078913	0.81[ASN][1000 genomes]
rs11078915	0.86[ASN][1000 genomes]
rs11654018	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs11655531	0.85[ASN][1000 genomes]
rs11657058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11657153	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11657899	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11658219	0.86[ASN][1000 genomes]
rs11658678	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs12150047	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs12449852	0.86[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs12450559	0.82[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs12452509	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs12452880	0.82[CHB][hapmap]
rs12600751	0.82[CHB][hapmap]
rs12936996	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs12937013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[ASN][1000 genomes]
rs12941619	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12942391	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947620	0.87[CHD][hapmap]
rs12952384	0.81[ASN][1000 genomes]
rs13341996	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs1619021	0.83[ASN][1000 genomes]
rs1874226	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877030	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303316	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs2338799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs35335692	0.86[ASN][1000 genomes]
rs364989	0.83[ASN][1000 genomes]
rs3764352	0.83[CEU][hapmap]
rs3889368	0.83[ASN][1000 genomes]
rs412430	0.83[ASN][1000 genomes]
rs4239222	0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs4332770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4357971	0.86[ASN][1000 genomes]
rs4390625	0.83[CHD][hapmap]
rs439537	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488484	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4511574	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs4591174	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794813	0.81[ASN][1000 genomes]
rs4794814	0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs4795356	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs4795357	0.82[CHB][hapmap]
rs4795358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4795367	0.83[ASN][1000 genomes]
rs4795369	0.85[CHD][hapmap]
rs4795375	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4795376	0.81[ASN][1000 genomes]
rs4795377	0.81[ASN][1000 genomes]
rs4795379	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795381	0.85[ASN][1000 genomes]
rs4795382	0.84[ASN][1000 genomes]
rs4795384	0.86[ASN][1000 genomes]
rs4795385	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55660616	0.83[ASN][1000 genomes]
rs6503503	0.82[CHB][hapmap]
rs6503504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6503507	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs6503513	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs6503519	0.86[ASN][1000 genomes]
rs6503520	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6503521	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208252	0.93[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7208487	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7212621	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs7216086	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs7221875	0.82[CHB][hapmap]
rs7223438	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7225096	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7406928	0.83[ASN][1000 genomes]
rs7501488	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7503069	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs7503377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7503514	0.81[ASN][1000 genomes]
rs7503705	0.82[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs8065963	0.82[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs8067511	0.82[ASN][1000 genomes]
rs8067884	0.81[ASN][1000 genomes]
rs8069074	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8073248	0.87[ASN][1000 genomes]
rs8074276	0.84[ASN][1000 genomes]
rs8074855	0.83[ASN][1000 genomes]
rs8075737	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8076494	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs8076546	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs8081528	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8182252	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879606	0.83[CEU][hapmap]
rs903507	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646419	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs9892055	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs9906612	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9908131	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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	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	nsv1057655	chr17:37333956-37732451	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer 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	44 gene(s)	inside rSNPs	diseases
7	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
8	nsv532712	chr17:37521822-37768345	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv1063848	chr17:37575622-37707592	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	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
11	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12947506	MYO1D	cis	parietal	SCAN
rs12947506	SLFN14	cis	parietal	SCAN
rs12947506	CCL4	cis	cerebellum	SCAN
rs12947506	GSDMA	cis	parietal	SCAN
rs12947506	DHRS11	cis	cerebellum	SCAN
rs12947506	PGAP3	cis	Thyroid	GTEx
rs12947506	SPACA3	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37683800-37719400	Weak transcription	Psoas Muscle	Psoas
2	chr17:37687800-37709600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:37687800-37729800	Weak transcription	Small Intestine	intestine
4	chr17:37688400-37708000	Weak transcription	Gastric	stomach
5	chr17:37688400-37709600	Weak transcription	Colonic Mucosa	Colon
6	chr17:37688400-37711600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:37688400-37711600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr17:37689000-37708000	Weak transcription	NH-A	brain
9	chr17:37689000-37719400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr17:37689200-37711600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr17:37690800-37709400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:37693000-37719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:37695400-37727400	Weak transcription	K562	blood
14	chr17:37695800-37707800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:37695800-37712400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr17:37695800-37723200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr17:37697400-37709600	Weak transcription	HMEC	breast
18	chr17:37699800-37714800	Strong transcription	Ovary	ovary
19	chr17:37700000-37708000	Weak transcription	Pancreas	Pancrea
20	chr17:37700200-37725800	Strong transcription	Placenta	Placenta
21	chr17:37700400-37709600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:37701000-37714600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr17:37701000-37714800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr17:37701000-37714800	Strong transcription	Brain Anterior Caudate	brain
25	chr17:37701000-37719400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:37701000-37728800	Strong transcription	Liver	Liver
27	chr17:37701200-37707600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:37701200-37708200	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr17:37701200-37710600	Strong transcription	Brain Hippocampus Middle	brain
30	chr17:37701200-37727600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr17:37701400-37708200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr17:37702400-37708600	Strong transcription	Brain Substantia Nigra	brain
33	chr17:37702400-37717600	Strong transcription	Thymus	Thymus
34	chr17:37702600-37709400	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr17:37702600-37710800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:37702600-37715000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:37702800-37710800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:37702800-37710800	Strong transcription	Brain Angular Gyrus	brain
39	chr17:37702800-37710800	Strong transcription	Brain Cingulate Gyrus	brain
40	chr17:37702800-37714400	Strong transcription	Fetal Intestine Large	intestine
41	chr17:37702800-37714600	Strong transcription	Lung	lung
42	chr17:37702800-37714800	Strong transcription	Fetal Thymus	thymus
43	chr17:37702800-37714800	Strong transcription	Spleen	Spleen
44	chr17:37702800-37716400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr17:37702800-37716600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr17:37702800-37717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr17:37702800-37718200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr17:37703200-37714800	Strong transcription	Primary T cells from cord blood	blood
49	chr17:37703800-37709800	Strong transcription	Esophagus	oesophagus
50	chr17:37703800-37714600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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