Variant report

Variant	rs12032905
Chromosome Location	chr1:228427643-228427644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228426358..228429102-chr1:228433065..228434825,2	MCF-7	breast:
2	chr1:228426928..228429804-chr1:228442378..228444505,2	MCF-7	breast:
3	chr1:228427134..228429598-chr1:228591173..228592748,2	K562	blood:

Variant related genes	Relation type
ENSG00000154358	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10916296	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12022027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12022323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12023522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12023551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12024329	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12024368	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12025837	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12026579	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12028729	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12028894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12029540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12029981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12030528	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12031017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12031390	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12031747	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12032850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12033588	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12033624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12034508	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12036437	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12036485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12037417	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12037423	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12037964	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12038090	1.00[AMR][1000 genomes]
rs12038612	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12039528	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12040123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12040394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12040506	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12041411	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12042084	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12043464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12044918	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12044962	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12048283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12049152	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12049530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12058217	1.00[JPT][hapmap]
rs12120597	1.00[AFR][1000 genomes]
rs1934882	1.00[JPT][hapmap]
rs2291999	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2298013	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28603121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754358	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55760713	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55946300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56384735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6693343	0.82[AMR][1000 genomes]
rs74144612	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	esv3372505	chr1:228424229-228428827	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:228413000-228428400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:228413000-228428800	Weak transcription	Gastric	stomach
5	chr1:228413600-228428800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:228413800-228428600	Weak transcription	Pancreas	Pancrea
7	chr1:228413800-228429000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:228414400-228430400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:228417200-228433000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:228418400-228436000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:228419600-228429600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:228420800-228428400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:228420800-228428800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:228422000-228428600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:228422200-228434800	ZNF genes & repeats	Dnd41	blood
16	chr1:228422400-228431000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
17	chr1:228422800-228428800	Weak transcription	Ovary	ovary
18	chr1:228423600-228428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:228423600-228429800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:228424200-228428200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:228424400-228428200	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:228424400-228429600	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr1:228424400-228430800	Strong transcription	Left Ventricle	heart
24	chr1:228424600-228428000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr1:228424600-228428400	Strong transcription	Primary T cells from cord blood	blood
26	chr1:228424600-228429400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:228424800-228428200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:228424800-228428400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:228425000-228428600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:228425400-228428600	Weak transcription	Adipose Nuclei	Adipose
31	chr1:228425600-228428800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:228425600-228429400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:228425600-228429400	ZNF genes & repeats	Thymus	Thymus
34	chr1:228425800-228429400	ZNF genes & repeats	Fetal Thymus	thymus
35	chr1:228425800-228434200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:228426000-228427800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
37	chr1:228426000-228427800	Strong transcription	Spleen	Spleen
38	chr1:228426000-228429400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:228426000-228435200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr1:228426200-228428000	ZNF genes & repeats	Fetal Intestine Large	intestine
41	chr1:228426200-228428000	Strong transcription	HSMMtube	muscle
42	chr1:228426200-228428600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:228426200-228429200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:228426400-228428000	Weak transcription	Lung	lung
45	chr1:228426400-228428400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:228426400-228428800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:228426400-228429200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr1:228426400-228429800	Strong transcription	Right Ventricle	heart
49	chr1:228426400-228430000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:228426600-228434400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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