Variant report

Variant	rs4768922
Chromosome Location	chr12:51179340-51179341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51156412..51159922-chr12:51179248..51181916,4	MCF-7	breast:
2	chr12:51168355..51171180-chr12:51178440..51181054,2	K562	blood:
3	chr12:51175977..51178519-chr12:51179089..51181352,2	MCF-7	breast:
4	chr12:51155325..51162343-chr12:51172009..51182370,14	MCF-7	breast:
5	chr12:51160285..51163042-chr12:51178907..51180859,2	MCF-7	breast:
6	chr12:51177098..51179722-chr12:51180352..51182751,3	K562	blood:
7	chr12:51177098..51179520-chr12:51179532..51182751,3	K562	blood:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10459235	0.88[ASN][1000 genomes]
rs10506294	0.84[ASW][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap]
rs10506295	0.86[CHB][hapmap]
rs10747587	0.84[ASW][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.80[AMR][1000 genomes]
rs10783382	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs10783384	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10783389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876065	0.86[GIH][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap]
rs10876070	0.93[GIH][hapmap];0.84[MEX][hapmap]
rs10876076	0.86[CHB][hapmap]
rs10876080	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876081	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876089	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876090	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876094	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876095	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169507	0.82[CHB][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap]
rs11169515	0.86[CHB][hapmap]
rs11169528	0.88[ASN][1000 genomes]
rs11169532	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11169537	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169538	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11169539	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11169544	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169552	1.00[ASW][hapmap];0.94[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];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169554	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615933	0.86[ASN][1000 genomes]
rs12231309	0.85[CHB][hapmap]
rs12424860	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580479	0.82[ASN][1000 genomes]
rs12809086	0.86[CHB][hapmap]
rs1344958	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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17124930	0.85[CHB][hapmap]
rs35845404	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3742063	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3742064	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3809319	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];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825402	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4026593	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4238108	0.86[CHB][hapmap]
rs4307773	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4768853	0.88[GIH][hapmap];0.84[MEX][hapmap]
rs4768866	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4768903	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs4768906	0.88[ASN][1000 genomes]
rs4768907	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4768911	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4768912	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4768913	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4768914	0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4768917	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768921	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768923	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768924	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768925	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4768940	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73094900	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73096846	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs864899	0.86[CHB][hapmap]
rs876078	0.84[ASW][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap]
rs952318	0.81[CHB][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3497481	chr12:51150734-51185125	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
2	esv3497482	chr12:51151798-51185232	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
3	esv3386327	chr12:51154734-51184232	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
4	nsv899077	chr12:51160612-51188397	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4768922	DIP2B	cis	Thyroid	GTEx
rs4768922	LASS5	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51159000-51180200	Weak transcription	Esophagus	oesophagus
2	chr12:51159200-51179400	Weak transcription	Aorta	Aorta
3	chr12:51159200-51192600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:51159400-51192600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:51159600-51189200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:51159800-51180600	Weak transcription	Fetal Lung	lung
7	chr12:51159800-51189600	Weak transcription	Spleen	Spleen
8	chr12:51159800-51190400	Weak transcription	Fetal Kidney	kidney
9	chr12:51159800-51191200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:51160000-51179800	Weak transcription	Small Intestine	intestine
11	chr12:51160000-51189800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:51160000-51190800	Weak transcription	Right Ventricle	heart
13	chr12:51160200-51179400	Weak transcription	Right Atrium	heart
14	chr12:51160200-51180200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:51160200-51189600	Weak transcription	Pancreas	Pancrea
16	chr12:51160200-51189800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:51160800-51189600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:51160800-51190600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:51161000-51189800	Weak transcription	Ovary	ovary
20	chr12:51161800-51180400	Weak transcription	Colonic Mucosa	Colon
21	chr12:51163200-51179800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:51164400-51189600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:51165400-51179800	Weak transcription	Brain Germinal Matrix	brain
24	chr12:51166800-51179600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:51167000-51180400	Weak transcription	Fetal Brain Female	brain
26	chr12:51167200-51179800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:51172600-51190600	Weak transcription	Fetal Brain Male	brain
28	chr12:51172800-51179400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:51173000-51189600	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:51173200-51190000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:51173600-51180200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:51174000-51180400	Strong transcription	Fetal Intestine Small	intestine
33	chr12:51174000-51181600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:51174200-51180000	Strong transcription	Fetal Stomach	stomach
35	chr12:51174800-51179400	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:51175000-51180200	Weak transcription	Lung	lung
37	chr12:51175000-51180400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:51175000-51180600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:51175400-51192200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:51176000-51179400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:51176000-51179400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:51176000-51179400	Weak transcription	Liver	Liver
43	chr12:51176000-51179400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr12:51176000-51180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:51176000-51180400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:51176000-51180600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:51176000-51180800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:51176000-51182600	Weak transcription	Brain Anterior Caudate	brain
49	chr12:51176000-51184400	Weak transcription	K562	blood
50	chr12:51176000-51189000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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