Variant report

Variant	rs2296378
Chromosome Location	chr1:180268476-180268477
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	chr1:180199261..180202253-chr1:180267146..180269079,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121454	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10158367	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10494527	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10737342	0.90[CHB][hapmap]
rs10753208	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10753209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10753211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753212	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798745	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs10798746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798756	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798757	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798760	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10798761	0.85[CHB][hapmap]
rs10798762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798766	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10798767	0.90[CHB][hapmap]
rs10798769	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10913968	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913969	0.80[CHB][hapmap]
rs10913973	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913974	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913976	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913978	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913982	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913983	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913984	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913986	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913987	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913994	0.81[CHB][hapmap]
rs10913998	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10914001	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10914002	0.90[CHB][hapmap]
rs10914005	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10914010	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10914014	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11580793	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11799870	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12034217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12039933	0.81[CHB][hapmap]
rs12091722	0.81[CHB][hapmap]
rs12121043	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12122338	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12127886	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12128560	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12129511	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12129784	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12131071	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12132837	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12135463	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12141348	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12141848	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12143350	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12404209	0.81[CHB][hapmap]
rs12405902	0.81[CHB][hapmap]
rs12561776	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12691484	0.90[CHB][hapmap]
rs12730889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12733492	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12749611	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1341924	0.81[CHB][hapmap]
rs1416821	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1418102	0.90[CHB][hapmap]
rs1925339	0.90[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2147774	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2764463	0.90[ASN][1000 genomes]
rs2877415	0.81[CHB][hapmap]
rs3845397	0.80[CHD][hapmap];0.82[GIH][hapmap]
rs3923222	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4058058	0.90[CHB][hapmap]
rs4076403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4142992	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4418555	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4420052	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4421553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4442335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4483365	0.90[CHB][hapmap]
rs4543756	0.81[CHB][hapmap]
rs4578179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4607831	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4634864	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4642852	0.90[CHB][hapmap]
rs4651064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4652493	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652496	0.90[CHB][hapmap]
rs4652498	0.90[CHB][hapmap]
rs4652499	0.90[CHB][hapmap]
rs4652504	0.83[ASN][1000 genomes]
rs4652505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425625	0.90[CHB][hapmap]
rs6425634	0.81[CHB][hapmap]
rs6661208	0.90[CHB][hapmap]
rs6665719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6670544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6674244	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6680368	0.90[CHB][hapmap]
rs6687442	0.81[ASN][1000 genomes]
rs6687549	0.80[ASN][1000 genomes]
rs6688844	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6697924	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6700986	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6704010	0.81[CEU][hapmap]
rs716760	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7523003	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7523857	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7528650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7532806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539910	0.90[CHB][hapmap]
rs822706	0.90[CHB][hapmap]
rs9726041	0.81[ASN][1000 genomes]
rs9730180	0.81[ASN][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	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2296378	ACBD6	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180240800-180270800	Weak transcription	NHLF	lung
2	chr1:180244200-180270400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:180244200-180278200	Weak transcription	HSMMtube	muscle
4	chr1:180245200-180282400	Weak transcription	Fetal Intestine Large	intestine
5	chr1:180245400-180280400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:180247800-180284200	Weak transcription	Fetal Thymus	thymus
7	chr1:180248800-180276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:180250400-180279800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:180250600-180278600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:180254400-180280400	Weak transcription	Fetal Stomach	stomach
11	chr1:180254800-180282400	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:180257400-180278200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:180257400-180278600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:180257600-180270600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:180257600-180289600	Weak transcription	Hela-S3	cervix
16	chr1:180257800-180278600	Weak transcription	HMEC	breast
17	chr1:180257800-180278600	Weak transcription	NHEK	skin
18	chr1:180257800-180279800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:180257800-180287200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:180257800-180296200	Weak transcription	Left Ventricle	heart
21	chr1:180258400-180285200	Weak transcription	Ovary	ovary
22	chr1:180259000-180271800	Weak transcription	Primary T cells from cord blood	blood
23	chr1:180259000-180278600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:180259400-180268800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:180261200-180284200	Weak transcription	K562	blood
26	chr1:180262200-180270400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:180262200-180276000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:180262400-180275000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:180262800-180280000	Weak transcription	Primary B cells from cord blood	blood
30	chr1:180263200-180269000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:180264000-180278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:180264200-180270000	Weak transcription	Fetal Intestine Small	intestine
33	chr1:180265600-180277600	Weak transcription	HepG2	liver
34	chr1:180266400-180269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:180266600-180269000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:180267000-180275400	Weak transcription	Dnd41	blood
37	chr1:180267000-180284400	Weak transcription	GM12878-XiMat	blood
38	chr1:180268000-180268600	Enhancers	A549	lung
39	chr1:180268000-180269000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:180268000-180269000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:180268200-180269200	Enhancers	Osteobl	bone
42	chr1:180268200-180269400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:180268200-180282800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:180268400-180269000	Enhancers	HSMM	muscle
45	chr1:180268400-180269200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr1:180268400-180269200	Enhancers	NHDF-Ad	bronchial

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