Variant report

Variant	rs2816184
Chromosome Location	chr1:179116784-179116785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1078872	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs10913690	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10913692	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913693	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10913695	0.87[ASN][1000 genomes]
rs10913697	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12130276	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs1325195	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1763022	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1826183	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1856968	0.82[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1858551	0.90[ASN][1000 genomes]
rs2066279	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2087559	0.88[ASN][1000 genomes]
rs2130576	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2171958	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2171959	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2258217	0.84[ASN][1000 genomes]
rs2258221	0.90[ASN][1000 genomes]
rs2306941	0.85[EUR][1000 genomes]
rs2486995	0.90[ASN][1000 genomes]
rs2486997	0.89[ASN][1000 genomes]
rs2486998	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2487563	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2493123	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2493124	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2636274	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2636275	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2636276	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2636277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2636280	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2636291	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636293	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2791936	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2791940	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2791941	0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2791942	0.88[ASN][1000 genomes]
rs2791943	0.92[ASN][1000 genomes]
rs2791944	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2791945	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2793790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2793793	0.88[ASN][1000 genomes]
rs2793794	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793795	0.86[ASN][1000 genomes]
rs2793796	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2793797	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2793798	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2793800	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2793801	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2793802	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2793803	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2793810	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2793813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2793816	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2816166	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2816183	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2816185	0.92[ASN][1000 genomes]
rs2816186	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs2816187	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2816189	0.88[ASN][1000 genomes]
rs2816190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs2816191	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2816193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs2816196	0.87[ASN][1000 genomes]
rs2816197	0.81[ASN][1000 genomes]
rs2816198	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2816199	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2816200	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2816201	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816202	0.81[ASN][1000 genomes]
rs2816203	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816207	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2816212	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2816213	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816214	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2816218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3121198	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3122376	0.80[EUR][1000 genomes]
rs36122838	0.86[ASN][1000 genomes]
rs3813642	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs3813643	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs3829794	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs411266	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs413613	0.88[EUR][1000 genomes]
rs451088	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs4651012	0.86[ASN][1000 genomes]
rs4651013	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs915337	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs9286921	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425839	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs965401	0.88[ASN][1000 genomes]
rs9662858	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9726961	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9727252	0.90[ASN][1000 genomes]
rs9728480	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs9729129	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9729199	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012667	chr1:179094571-179120280	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002253	chr1:179094571-179120938	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1001191	chr1:179097246-179120938	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1009493	chr1:179110523-179121079	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2816184	FAM20B	cis	parietal	SCAN
rs2816184	CACYBP	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179093400-179117200	Weak transcription	Fetal Stomach	stomach
2	chr1:179099600-179116800	Weak transcription	Thymus	Thymus
3	chr1:179099600-179119400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:179099600-179122600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:179100000-179121000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:179100600-179117200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:179107600-179119800	Weak transcription	Liver	Liver
8	chr1:179110000-179118400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:179110200-179121400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:179111000-179118200	Weak transcription	Primary B cells from cord blood	blood
11	chr1:179111400-179117400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:179111400-179118400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:179111400-179121400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:179111400-179121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:179112200-179118800	Weak transcription	Fetal Intestine Large	intestine
16	chr1:179112200-179121800	Weak transcription	Adipose Nuclei	Adipose
17	chr1:179112200-179121800	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:179112200-179124600	Weak transcription	Left Ventricle	heart
19	chr1:179112400-179117200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:179112400-179117400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:179112400-179117400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:179112400-179117600	Weak transcription	Right Ventricle	heart
23	chr1:179112400-179118400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:179112400-179119600	Weak transcription	HepG2	liver
25	chr1:179112400-179121000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:179112400-179121200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:179112400-179121400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:179112400-179121400	Weak transcription	Small Intestine	intestine
29	chr1:179112400-179121600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:179112400-179133000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:179112400-179139000	Weak transcription	K562	blood
32	chr1:179112800-179116800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:179112800-179117200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:179112800-179119000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:179113200-179116800	Enhancers	HUVEC	blood vessel
36	chr1:179113200-179133000	Weak transcription	Hela-S3	cervix
37	chr1:179113600-179117400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:179113600-179121600	Weak transcription	Ovary	ovary
39	chr1:179113800-179121200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:179114200-179119800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:179115000-179119600	Weak transcription	A549	lung
42	chr1:179115600-179116800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:179115600-179121000	Weak transcription	Primary T cells from cord blood	blood
44	chr1:179116000-179121200	Weak transcription	Psoas Muscle	Psoas
45	chr1:179116000-179121600	Weak transcription	Fetal Heart	heart
46	chr1:179116200-179117600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:179116200-179118400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:179116200-179118600	Weak transcription	NH-A	brain
49	chr1:179116200-179120200	Weak transcription	NHEK	skin
50	chr1:179116200-179121000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links