Variant report

Variant	rs4242870
Chromosome Location	chr12:82747392-82747393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:82743772-82747430	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:82746956-82747457	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
METTL25	TF binding region

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10219540	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs10431469	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10732677	0.84[EUR][1000 genomes]
rs10735451	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10735454	1.00[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10735455	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs10746241	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10746243	0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs10746247	0.84[EUR][1000 genomes]
rs10746248	0.84[EUR][1000 genomes]
rs10746250	0.84[EUR][1000 genomes]
rs10778891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10778894	0.84[EUR][1000 genomes]
rs10778897	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs10778903	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs10778904	0.84[EUR][1000 genomes]
rs10778905	0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs10778906	0.88[YRI][hapmap]
rs10778908	0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs10862481	0.84[EUR][1000 genomes]
rs10862484	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10862485	0.84[EUR][1000 genomes]
rs10862486	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs17009470	0.84[EUR][1000 genomes]
rs17719033	0.84[EUR][1000 genomes]
rs17773980	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17775000	0.84[EUR][1000 genomes]
rs17775447	0.84[EUR][1000 genomes]
rs17775501	0.84[EUR][1000 genomes]
rs1874058	0.81[YRI][hapmap]
rs2068633	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254688	0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs2401026	0.84[EUR][1000 genomes]
rs2401027	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2401032	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs2401036	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2401039	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs2401040	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2642015	0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs2642017	0.84[EUR][1000 genomes]
rs2642018	0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs2642019	0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs2642023	0.83[YRI][hapmap]
rs2717449	0.88[YRI][hapmap]
rs2717459	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs2731286	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs2731290	0.87[YRI][hapmap]
rs2731291	0.87[YRI][hapmap]
rs2731292	0.88[YRI][hapmap]
rs2731295	0.85[YRI][hapmap]
rs2731297	0.82[EUR][1000 genomes]
rs28626834	0.84[EUR][1000 genomes]
rs2895910	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs2895911	0.84[EUR][1000 genomes]
rs2895912	0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs2895915	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs4143187	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs4143190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4242864	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4257045	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4284465	0.84[EUR][1000 genomes]
rs4296098	0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs4334093	0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs4343090	0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs4356298	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs4370996	0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs4387422	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs4399377	0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs4417379	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs4460874	0.84[EUR][1000 genomes]
rs4471506	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4483662	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4505128	0.94[YRI][hapmap];0.84[EUR][1000 genomes]
rs4517594	0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs4540892	0.84[EUR][1000 genomes]
rs4553425	0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs4587790	0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs4628747	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs4882379	0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs4882386	0.84[EUR][1000 genomes]
rs4882389	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs4882390	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs4882435	0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs4882438	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4882541	0.84[EUR][1000 genomes]
rs55720165	0.93[EUR][1000 genomes]
rs55887136	0.84[EUR][1000 genomes]
rs56337649	0.84[EUR][1000 genomes]
rs6539669	0.84[EUR][1000 genomes]
rs7294771	0.84[EUR][1000 genomes]
rs7294903	0.84[EUR][1000 genomes]
rs7297164	0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs7299307	0.81[AFR][1000 genomes]
rs7299616	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs7309442	0.84[EUR][1000 genomes]
rs7313975	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs7315834	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7316500	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs7954460	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs7969953	0.84[EUR][1000 genomes]
rs7977443	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8181688	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs8181705	0.94[YRI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559539	chr12:82280797-82896218	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1041954	chr12:82314981-83008609	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv541550	chr12:82314981-83008609	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv832471	chr12:82578953-82755360	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription 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	21 gene(s)	inside rSNPs	diseases
6	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82740200-82751600	Weak transcription	Gastric	stomach
2	chr12:82740800-82750000	Weak transcription	Fetal Intestine Small	intestine
3	chr12:82740800-82750000	Weak transcription	Psoas Muscle	Psoas
4	chr12:82741000-82749400	Weak transcription	Fetal Brain Male	brain
5	chr12:82741200-82751000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:82741400-82749400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:82741600-82749200	Strong transcription	Adipose Nuclei	Adipose
8	chr12:82741600-82749800	Strong transcription	Primary T cells from cord blood	blood
9	chr12:82741800-82747800	Strong transcription	Brain Hippocampus Middle	brain
10	chr12:82742000-82749400	Strong transcription	Liver	Liver
11	chr12:82742000-82750000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:82742200-82749400	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:82742400-82750000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:82742400-82750000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr12:82742600-82747800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr12:82742600-82748600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:82742600-82749200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:82742600-82750800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:82742600-82751400	Weak transcription	Aorta	Aorta
20	chr12:82742600-82751600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:82742600-82751600	Weak transcription	Spleen	Spleen
22	chr12:82742800-82747400	Strong transcription	Primary B cells from cord blood	blood
23	chr12:82742800-82751200	Weak transcription	Colonic Mucosa	Colon
24	chr12:82742800-82751600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:82743400-82748800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:82743400-82750600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr12:82743400-82750600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr12:82743400-82750600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:82743400-82751000	Weak transcription	Right Ventricle	heart
30	chr12:82743600-82749800	Weak transcription	Brain Angular Gyrus	brain
31	chr12:82743600-82750000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr12:82743600-82750000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr12:82743800-82749000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:82743800-82750800	Weak transcription	HSMMtube	muscle
35	chr12:82743800-82751600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:82743800-82751600	Weak transcription	Esophagus	oesophagus
37	chr12:82744000-82748800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr12:82744000-82749200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:82744000-82749400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:82744000-82749400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:82744000-82749600	Weak transcription	HepG2	liver
42	chr12:82744000-82750200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:82744000-82750200	Weak transcription	Fetal Heart	heart
44	chr12:82744000-82750600	Strong transcription	Fetal Thymus	thymus
45	chr12:82744200-82751200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr12:82744400-82748200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:82744400-82750800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:82744600-82748200	Strong transcription	Brain Anterior Caudate	brain
49	chr12:82744600-82750000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:82744800-82750000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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