Variant report

Variant	rs11571409
Chromosome Location	chr12:1040219-1040220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1036843..1040393-chr12:1058152..1060632,3	K562	blood:
2	chr12:1039000..1041296-chr12:1058261..1060120,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000002016	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10744729	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849578	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849584	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11064580	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11064585	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11064593	0.99[ASN][1000 genomes]
rs11226	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11571448	0.98[ASN][1000 genomes]
rs11611051	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11614499	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12581940	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2255390	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2269937	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286029	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3748521	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766370	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4980974	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6413436	0.93[ASN][1000 genomes]
rs7296555	0.90[ASN][1000 genomes]
rs7300444	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7300718	0.99[ASN][1000 genomes]
rs7301931	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7303748	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308979	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7310449	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7964502	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs953361	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
18	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
19	nsv1041675	chr12:993822-1091354	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
20	nsv470256	chr12:998365-1438761	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
21	nsv492321	chr12:1011692-1388512	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
22	nsv898579	chr12:1013176-1510505	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
23	nsv898580	chr12:1024688-1569097	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11571409	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:964400-1042200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:986200-1042200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:987000-1041200	Strong transcription	Fetal Intestine Large	intestine
4	chr12:989200-1042200	Strong transcription	Fetal Muscle Leg	muscle
5	chr12:1004400-1041200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:1020800-1054600	Strong transcription	Fetal Intestine Small	intestine
7	chr12:1023800-1041000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:1024600-1055800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:1024800-1042200	Strong transcription	Fetal Thymus	thymus
10	chr12:1024800-1042200	Strong transcription	Dnd41	blood
11	chr12:1024800-1043200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:1024800-1057400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:1026000-1042200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:1026200-1043200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:1026400-1042200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:1026400-1042400	Strong transcription	Fetal Stomach	stomach
17	chr12:1026400-1042600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:1026400-1048200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:1026600-1055800	Weak transcription	K562	blood
20	chr12:1029600-1040600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:1029600-1041200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:1029600-1042200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr12:1029800-1041200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:1029800-1041600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:1029800-1041600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:1029800-1042200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr12:1029800-1042400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:1030000-1042000	Strong transcription	Liver	Liver
29	chr12:1030000-1042200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:1030000-1042600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr12:1030200-1042400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:1030400-1042200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:1030400-1042200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:1030600-1042200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:1031200-1042200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:1031400-1041200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:1031400-1041200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:1031400-1042200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:1031600-1041400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr12:1032000-1041200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:1032000-1041600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:1032400-1041200	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr12:1032400-1042200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:1032400-1042200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:1032400-1042200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:1032800-1041200	Strong transcription	Brain Cingulate Gyrus	brain
47	chr12:1032800-1042200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr12:1033000-1041200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr12:1033000-1042200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:1033000-1042200	Strong transcription	Brain Hippocampus Middle	brain

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