Variant report

Variant	rs2900499
Chromosome Location	chr12:106880963-106880964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106874061..106876489-chr12:106880946..106882862,2	MCF-7	breast:
2	chr12:106880850..106882517-chr12:106891803..106893326,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10444532	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10746060	0.86[EUR][1000 genomes]
rs10778465	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10778466	0.86[EUR][1000 genomes]
rs10778468	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10778469	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10778471	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10778473	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10778474	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10778476	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10778485	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861577	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10861578	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10861579	0.86[EUR][1000 genomes]
rs10861581	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs10861582	0.81[EUR][1000 genomes]
rs10861585	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10861586	0.83[EUR][1000 genomes]
rs10861592	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10861593	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10861595	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10861601	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10861605	0.87[EUR][1000 genomes]
rs10861608	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10861614	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112945	0.86[EUR][1000 genomes]
rs11112949	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11112953	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11112961	0.91[EUR][1000 genomes]
rs11112971	0.86[EUR][1000 genomes]
rs11112979	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11112980	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112990	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11112991	0.84[EUR][1000 genomes]
rs11112992	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112993	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11113003	0.87[EUR][1000 genomes]
rs11113004	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11113009	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11113011	1.00[ASN][1000 genomes]
rs11113024	1.00[ASN][1000 genomes]
rs11609315	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11611176	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12305705	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12312915	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12423068	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12425459	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17038414	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17221107	0.89[ASN][1000 genomes]
rs17285274	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2141774	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288268	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2374606	0.81[EUR][1000 genomes]
rs2374610	0.92[EUR][1000 genomes]
rs28475238	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2900500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851631	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3851632	0.85[EUR][1000 genomes]
rs4522273	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4625578	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55678155	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55689816	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61941917	0.86[EUR][1000 genomes]
rs61941918	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61941920	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61941921	0.87[EUR][1000 genomes]
rs61941943	0.88[EUR][1000 genomes]
rs61941944	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61943670	0.86[EUR][1000 genomes]
rs61943690	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6539268	0.86[EUR][1000 genomes]
rs67966244	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7132744	0.84[EUR][1000 genomes]
rs7134615	0.85[EUR][1000 genomes]
rs7136098	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7139139	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7296090	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7307711	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7309020	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7971581	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2900499	POLR3B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:106853400-106886400	Weak transcription	Fetal Kidney	kidney
3	chr12:106854200-106886800	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:106854400-106904800	Weak transcription	HSMM	muscle
5	chr12:106854600-106899800	Weak transcription	Fetal Thymus	thymus
6	chr12:106855800-106895600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:106855800-106896200	Weak transcription	Thymus	Thymus
8	chr12:106856000-106893000	Weak transcription	Right Ventricle	heart
9	chr12:106856800-106884000	Weak transcription	NHEK	skin
10	chr12:106856800-106889400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:106856800-106899400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:106857200-106890200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:106858600-106895400	Weak transcription	Fetal Heart	heart
14	chr12:106859200-106882800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:106865200-106881800	Weak transcription	Pancreas	Pancrea
16	chr12:106865200-106889800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:106865200-106890600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr12:106865200-106892400	Weak transcription	Aorta	Aorta
19	chr12:106865400-106887600	Weak transcription	Fetal Stomach	stomach
20	chr12:106865400-106888000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:106865400-106889200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:106865400-106889200	Weak transcription	Lung	lung
23	chr12:106865400-106889200	Weak transcription	Ovary	ovary
24	chr12:106865400-106889400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:106865400-106889400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:106865400-106889800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:106865400-106889800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:106865400-106890400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:106865400-106890400	Weak transcription	Colonic Mucosa	Colon
30	chr12:106865400-106890400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:106865400-106891800	Weak transcription	Gastric	stomach
32	chr12:106865400-106893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:106865400-106895200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:106865400-106897800	Weak transcription	Spleen	Spleen
35	chr12:106865600-106889200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr12:106865600-106889400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr12:106865600-106889400	Weak transcription	Adipose Nuclei	Adipose
38	chr12:106865600-106889800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:106865600-106890200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:106865600-106890200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:106865600-106890400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:106865600-106890400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:106865600-106890400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:106865600-106890400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr12:106865600-106890400	Weak transcription	Dnd41	blood
46	chr12:106865600-106891000	Weak transcription	Brain Angular Gyrus	brain
47	chr12:106865600-106891200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:106865600-106891400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:106865600-106891400	Weak transcription	Fetal Lung	lung
50	chr12:106865600-106891600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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