Variant report

Variant	rs4980972
Chromosome Location	chr12:963195-963196
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1012729	0.84[EUR][1000 genomes]
rs1051669	0.82[EUR][1000 genomes]
rs10735063	0.80[ASN][1000 genomes]
rs10735065	0.98[ASN][1000 genomes]
rs10774459	0.80[ASN][1000 genomes]
rs10774463	0.91[ASN][1000 genomes]
rs10774466	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10849562	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10849563	0.98[ASN][1000 genomes]
rs10849568	0.98[ASN][1000 genomes]
rs10849583	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11064560	0.98[ASN][1000 genomes]
rs11064582	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11064584	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11513723	0.81[EUR][1000 genomes]
rs1159744	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11829138	0.82[EUR][1000 genomes]
rs11832907	0.82[EUR][1000 genomes]
rs1970996	0.98[ASN][1000 genomes]
rs1990021	0.95[ASN][1000 genomes]
rs2014160	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2051852	0.82[EUR][1000 genomes]
rs2107612	0.80[ASN][1000 genomes]
rs2107614	0.91[ASN][1000 genomes]
rs2158502	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240282	0.98[ASN][1000 genomes]
rs2240283	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301880	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2369490	0.88[ASN][1000 genomes]
rs2369491	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4388955	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4766377	0.80[EUR][1000 genomes]
rs4980969	0.98[ASN][1000 genomes]
rs4980970	0.98[ASN][1000 genomes]
rs6489749	0.91[ASN][1000 genomes]
rs6489751	0.95[ASN][1000 genomes]
rs6489752	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6489754	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6489757	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67969314	0.95[ASN][1000 genomes]
rs724709	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7298001	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7300056	0.98[ASN][1000 genomes]
rs7301349	0.98[ASN][1000 genomes]
rs7309858	0.95[ASN][1000 genomes]
rs7311065	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7311423	0.98[ASN][1000 genomes]
rs765250	0.95[ASN][1000 genomes]
rs7953912	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7959921	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7966632	0.91[ASN][1000 genomes]
rs7971329	0.98[ASN][1000 genomes]
rs7972490	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7980163	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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 target site	80 gene(s)	inside rSNPs	diseases
4	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
8	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
9	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv898568	chr12:547683-969800	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
12	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
13	nsv1051590	chr12:722215-974773	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv541338	chr12:722215-974773	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
15	nsv468956	chr12:737230-982321	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer 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	26 gene(s)	inside rSNPs	diseases
16	nsv556893	chr12:737230-982321	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	esv2757485	chr12:786238-964551	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
18	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
19	esv2753658	chr12:835074-964506	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
20	esv3693103	chr12:837113-971317	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
21	nsv556898	chr12:850288-968489	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
22	nsv556900	chr12:854331-968489	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
23	esv2752382	chr12:863833-964506	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
25	nsv898577	chr12:873890-969800	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv1042333	chr12:907975-1081509	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
27	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
28	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
29	nsv522901	chr12:922408-968489	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
30	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4980972	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:905400-970200	Weak transcription	Spleen	Spleen
2	chr12:914400-971000	Weak transcription	Right Ventricle	heart
3	chr12:916400-977200	Weak transcription	Gastric	stomach
4	chr12:920200-966800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:928200-994400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:933600-966600	Weak transcription	Fetal Brain Female	brain
7	chr12:933600-971400	Weak transcription	Fetal Brain Male	brain
8	chr12:934600-970200	Weak transcription	Colonic Mucosa	Colon
9	chr12:939600-967400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:939600-968800	Weak transcription	Lung	lung
11	chr12:939600-977000	Weak transcription	Pancreas	Pancrea
12	chr12:940000-969200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:940400-969000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:940400-971400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:940600-966400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:940800-963800	Weak transcription	Fetal Stomach	stomach
17	chr12:940800-966800	Weak transcription	Fetal Intestine Small	intestine
18	chr12:942800-966400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:943600-966000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:943800-965800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:943800-965800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:943800-966000	Weak transcription	Placenta	Placenta
23	chr12:943800-966200	Weak transcription	Fetal Intestine Large	intestine
24	chr12:943800-966400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:943800-966600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:944000-966400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:944000-969800	Weak transcription	K562	blood
28	chr12:944400-966000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:945200-971000	Weak transcription	Psoas Muscle	Psoas
30	chr12:948400-965800	Weak transcription	Primary B cells from cord blood	blood
31	chr12:951200-965800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:953000-966200	Weak transcription	Thymus	Thymus
33	chr12:953800-966000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:954800-966200	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:955000-963800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:955000-965800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr12:955000-965800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:955600-966000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:955800-965800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:955800-966000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:955800-966600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:957400-970400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:957600-970000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:957600-970200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:958400-966000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:958600-966200	Weak transcription	HepG2	liver
47	chr12:958600-972000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr12:958800-964400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:958800-966000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:958800-966200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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