Variant report

Variant	rs12128041
Chromosome Location	chr1:78209205-78209206
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	chr1:78207734..78210591-chr1:78224794..78227087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077254	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10873950	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap]
rs10873951	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11162369	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1166585	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1166586	0.88[CEU][hapmap]
rs1166588	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12074409	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs12142671	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1565850	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs1565851	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs1962523	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2029768	0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs2147318	0.88[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2172727	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs2274123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278838	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs278845	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278847	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs278852	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs278854	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278862	1.00[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3509	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs371076	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3767030	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs4245658	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs4589153	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4600093	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4949658	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs4949659	0.94[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs4949809	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4949811	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs4949816	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs5025902	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56688304	0.81[EUR][1000 genomes]
rs6603955	0.82[EUR][1000 genomes]
rs6667519	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap]
rs6667803	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs6675743	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6687596	0.81[EUR][1000 genomes]
rs6693100	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs728741	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs7513619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7521042	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7524866	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs7531286	0.89[CHB][hapmap]
rs872342	0.80[CHD][hapmap];0.89[JPT][hapmap]
rs9662527	0.83[CEU][hapmap]

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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv1796958	chr1:78138955-78267421	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1798160	chr1:78149941-78267421	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv508326	chr1:78184379-78234247	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12128041	AK5	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78173800-78224400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:78182400-78210200	Weak transcription	Psoas Muscle	Psoas
3	chr1:78182800-78210200	Weak transcription	Right Ventricle	heart
4	chr1:78189400-78210200	Weak transcription	NHEK	skin
5	chr1:78190600-78210800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:78191600-78210400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:78191600-78215600	Weak transcription	A549	lung
8	chr1:78192000-78215000	Weak transcription	HSMMtube	muscle
9	chr1:78192200-78222400	Weak transcription	Brain Substantia Nigra	brain
10	chr1:78193000-78221200	Weak transcription	Brain Angular Gyrus	brain
11	chr1:78193600-78222600	Weak transcription	Fetal Kidney	kidney
12	chr1:78194400-78214400	Weak transcription	NHLF	lung
13	chr1:78194400-78223400	Weak transcription	NH-A	brain
14	chr1:78194600-78215200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:78194800-78212600	Weak transcription	Colonic Mucosa	Colon
16	chr1:78195000-78213000	Weak transcription	HepG2	liver
17	chr1:78195200-78210200	Weak transcription	Pancreas	Pancrea
18	chr1:78195200-78210400	Weak transcription	Lung	lung
19	chr1:78195200-78214000	Weak transcription	Small Intestine	intestine
20	chr1:78195400-78213000	Weak transcription	Aorta	Aorta
21	chr1:78195400-78216000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:78195400-78216800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:78195400-78222200	Weak transcription	Gastric	stomach
24	chr1:78195400-78223200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:78195400-78224200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:78195400-78224800	Weak transcription	Spleen	Spleen
27	chr1:78196800-78221800	Weak transcription	Ovary	ovary
28	chr1:78197400-78213200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:78197800-78215000	Weak transcription	Fetal Stomach	stomach
30	chr1:78197800-78221800	Weak transcription	Thymus	Thymus
31	chr1:78197800-78222400	Weak transcription	Fetal Intestine Small	intestine
32	chr1:78197800-78223400	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:78198200-78222200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:78198400-78212200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:78198400-78213000	Weak transcription	Stomach Mucosa	stomach
36	chr1:78198400-78224000	Weak transcription	Esophagus	oesophagus
37	chr1:78200200-78218800	Weak transcription	HUVEC	blood vessel
38	chr1:78202800-78217000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:78203800-78210200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:78205000-78210000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:78205200-78210200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:78205200-78214600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:78205400-78220200	Weak transcription	GM12878-XiMat	blood
44	chr1:78205400-78221800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:78205600-78213000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:78205600-78222200	Weak transcription	Fetal Brain Male	brain
47	chr1:78205800-78210200	Weak transcription	HMEC	breast
48	chr1:78205800-78213000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:78205800-78213600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:78206000-78210200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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