Variant report

Variant	rs12044161
Chromosome Location	chr1:185066458-185066459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185014298..185015866-chr1:185065926..185068638,2	K562	blood:
2	chr1:185062925..185066801-chr1:185070030..185072676,4	K562	blood:
3	chr1:185064872..185066724-chr1:185124561..185126369,2	MCF-7	breast:
4	chr1:185052742..185055562-chr1:185064799..185067162,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121481	Chromatin interaction
ENSG00000121486	Chromatin interaction
ENSG00000116668	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1008502	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1046592	1.00[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs10489581	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10797997	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10797998	1.00[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10911676	0.92[EUR][1000 genomes]
rs10911682	0.85[EUR][1000 genomes]
rs10911686	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12022419	1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12023744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025995	0.90[EUR][1000 genomes]
rs12026000	0.90[EUR][1000 genomes]
rs12027607	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12028809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12030778	0.90[EUR][1000 genomes]
rs12030967	0.97[EUR][1000 genomes]
rs12031837	0.90[EUR][1000 genomes]
rs12035073	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12035433	0.90[EUR][1000 genomes]
rs12037466	0.83[EUR][1000 genomes]
rs12037692	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12039541	0.83[EUR][1000 genomes]
rs12040650	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12041374	0.90[EUR][1000 genomes]
rs12043427	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12043495	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12043561	0.90[EUR][1000 genomes]
rs12043617	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12044997	0.97[EUR][1000 genomes]
rs12045772	0.97[EUR][1000 genomes]
rs12046095	0.90[EUR][1000 genomes]
rs12046202	0.97[EUR][1000 genomes]
rs12046801	0.92[EUR][1000 genomes]
rs12049293	0.88[EUR][1000 genomes]
rs12064938	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12086086	1.00[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs12094983	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12401293	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12404644	1.00[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12408279	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12408500	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12409926	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs1407554	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1544052	1.00[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs16865296	0.97[EUR][1000 genomes]
rs2273881	0.85[EUR][1000 genomes]
rs3766719	1.00[GIH][hapmap]
rs3766720	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs3766723	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs3806243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41264588	0.85[EUR][1000 genomes]
rs41264590	0.90[EUR][1000 genomes]
rs56107433	0.90[EUR][1000 genomes]
rs61125463	0.90[EUR][1000 genomes]
rs61495015	0.90[EUR][1000 genomes]
rs72724103	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72724108	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72739677	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72739679	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72741807	0.90[EUR][1000 genomes]
rs72741808	0.90[EUR][1000 genomes]
rs72741816	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72741817	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72741819	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking 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 miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185016400-185067200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:185016400-185073800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:185018400-185101800	Weak transcription	Fetal Brain Male	brain
4	chr1:185030200-185076600	Weak transcription	Gastric	stomach
5	chr1:185034800-185077000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:185043600-185069400	Weak transcription	Pancreas	Pancrea
7	chr1:185045000-185068800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:185050000-185067200	Weak transcription	Fetal Heart	heart
9	chr1:185052000-185076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:185052400-185074800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:185052800-185070800	Weak transcription	Small Intestine	intestine
12	chr1:185052800-185076600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:185053200-185067200	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:185053600-185070800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:185054200-185073200	Weak transcription	Brain Anterior Caudate	brain
16	chr1:185054200-185073800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:185054400-185101800	Weak transcription	A549	lung
18	chr1:185054600-185068800	Weak transcription	Brain Angular Gyrus	brain
19	chr1:185054800-185072400	Weak transcription	HepG2	liver
20	chr1:185055000-185070200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:185055200-185067400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:185055200-185070200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:185055200-185076600	Weak transcription	Lung	lung
24	chr1:185055400-185067200	Weak transcription	GM12878-XiMat	blood
25	chr1:185055400-185069200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:185055400-185096200	Weak transcription	Hela-S3	cervix
27	chr1:185055600-185067200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:185055600-185067200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:185055800-185067200	Weak transcription	Spleen	Spleen
30	chr1:185056000-185076800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:185056200-185072400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:185056200-185074200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:185056200-185124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:185056400-185071400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:185056400-185073800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:185056400-185074000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:185056600-185069400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:185056600-185069800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:185056600-185074000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:185056600-185077000	Weak transcription	Thymus	Thymus
41	chr1:185057200-185073400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:185057200-185074000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:185057600-185094600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:185058200-185074800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:185058400-185067200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:185058600-185067200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:185058600-185072800	Weak transcription	NHLF	lung
48	chr1:185058600-185089000	Weak transcription	Ovary	ovary
49	chr1:185058800-185069600	Weak transcription	Brain Substantia Nigra	brain
50	chr1:185058800-185075800	Weak transcription	Brain Inferior Temporal Lobe	brain

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