Variant report

Variant	rs12298484
Chromosome Location	chr12:124418674-124418675
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	chr12:124408910..124411445-chr12:124416040..124418769,2	MCF-7	breast:
2	chr12:124409871..124412638-chr12:124416251..124418767,2	K562	blood:

Variant related genes	Relation type
ENSG00000270028	Chromatin interaction
ENSG00000197653	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1054852	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs10846577	0.92[CHB][hapmap];0.94[CHD][hapmap]
rs10846578	1.00[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs10846579	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057393	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057399	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11057400	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11057401	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11057407	0.91[EUR][1000 genomes]
rs11057408	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11057409	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11057412	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11057413	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11831913	0.92[CEU][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11833002	0.99[EUR][1000 genomes]
rs11835839	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11837287	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1187415	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs12296259	0.98[EUR][1000 genomes]
rs12301673	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12303671	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12303933	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12310367	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12311114	0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12311848	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12316080	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12317176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12809125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12809473	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12823740	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs12824567	0.92[CEU][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes]
rs12827409	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12829951	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12833624	0.96[EUR][1000 genomes]
rs1882491	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2130382	0.92[CEU][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes]
rs2178663	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3186071	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34114498	0.97[EUR][1000 genomes]
rs34180676	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34854841	0.91[EUR][1000 genomes]
rs34878139	0.99[EUR][1000 genomes]
rs35099862	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35825716	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3789967	0.97[EUR][1000 genomes]
rs3802999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4405410	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4575361	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4765127	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4765148	0.92[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs4765219	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4765305	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4765335	0.90[EUR][1000 genomes]
rs4765528	0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs4765541	0.97[EUR][1000 genomes]
rs4765562	0.97[EUR][1000 genomes]
rs4930721	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930722	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4930723	1.00[CEU][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4930724	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs4930725	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4930726	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55990776	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56041971	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6488912	0.99[EUR][1000 genomes]
rs6488913	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6488914	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7131882	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7132655	1.00[CEU][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7133378	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7134121	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7135314	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71458830	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7301953	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7305864	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7307053	0.93[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs7307277	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7311233	0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7311969	1.00[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs7312404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7955815	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7958691	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7961449	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7966192	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7973683	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs7975482	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7978610	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs952632	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9863	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9971695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12298484	SRRM4	cis	parietal	SCAN
rs12298484	CCDC92	cis	cerebellum	SCAN
rs12298484	CCDC92	cis	Heart Left Ventricle	GTEx
rs12298484	RP11-380L11.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124407400-124422000	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr12:124408800-124428000	Weak transcription	Right Atrium	heart
3	chr12:124409400-124419600	Weak transcription	Right Ventricle	heart
4	chr12:124409600-124426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:124409800-124419400	Weak transcription	Brain Anterior Caudate	brain
6	chr12:124410400-124420600	Weak transcription	Pancreas	Pancrea
7	chr12:124410800-124419200	Weak transcription	Brain Substantia Nigra	brain
8	chr12:124410800-124420600	Weak transcription	Brain Angular Gyrus	brain
9	chr12:124411200-124420600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:124412000-124420400	Enhancers	Fetal Thymus	thymus
11	chr12:124412800-124420400	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:124413000-124418800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:124414000-124418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:124415000-124419000	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:124415000-124419000	Weak transcription	HSMMtube	muscle
16	chr12:124415000-124423000	Weak transcription	HSMM	muscle
17	chr12:124415200-124419000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:124415800-124419000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:124416000-124419400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:124416400-124420200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:124416600-124421200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:124416800-124419800	Weak transcription	Lung	lung
23	chr12:124416800-124420600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:124417000-124419000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr12:124417000-124419800	Enhancers	Thymus	Thymus
26	chr12:124417000-124420400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:124417200-124420600	Weak transcription	NHLF	lung
28	chr12:124417200-124421800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:124417200-124424400	Weak transcription	Colonic Mucosa	Colon
30	chr12:124417400-124420400	Weak transcription	Fetal Lung	lung
31	chr12:124417400-124421000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:124417400-124421800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:124417400-124421800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:124417400-124421800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:124417400-124421800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:124417400-124421800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:124417400-124422000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:124417600-124419200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:124417600-124419200	Weak transcription	Adipose Nuclei	Adipose
40	chr12:124417600-124419200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:124417600-124420400	Weak transcription	Primary T cells from cord blood	blood
42	chr12:124417600-124420400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:124417600-124421000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:124417600-124443600	Weak transcription	Fetal Kidney	kidney
45	chr12:124417800-124419000	Weak transcription	Aorta	Aorta
46	chr12:124417800-124419200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:124417800-124421200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:124417800-124422000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:124417800-124427400	Weak transcription	Fetal Brain Male	brain
50	chr12:124417800-124428400	Strong transcription	Brain Germinal Matrix	brain

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