Variant report

Variant	rs12030852
Chromosome Location	chr1:228882701-228882702
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228882022..228883685-chr1:228887134..228889075,2	MCF-7	breast:
2	chr1:228878069..228881022-chr1:228881765..228883502,2	MCF-7	breast:
3	chr1:228877885..228881410-chr1:228882153..228885594,3	K562	blood:

Variant related genes	Relation type
ENSG00000116574	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12024625	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68014968	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750025	0.83[AMR][1000 genomes]
rs72751913	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751940	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv468316	chr1:228854703-228919202	Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv549300	chr1:228854703-228919202	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228872600-228884400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:228873200-228884800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:228873800-228882800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:228873800-228884200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:228873800-228884200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:228874400-228884000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:228875000-228884200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:228875600-228883200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr1:228875800-228884000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:228876200-228883200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:228876600-228883400	Strong transcription	Fetal Intestine Small	intestine
12	chr1:228876800-228884800	Weak transcription	Fetal Brain Male	brain
13	chr1:228877000-228883200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:228877000-228884800	Weak transcription	Fetal Kidney	kidney
15	chr1:228877200-228883600	Strong transcription	Fetal Stomach	stomach
16	chr1:228877200-228889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:228877400-228883800	Strong transcription	Fetal Brain Female	brain
18	chr1:228877600-228883600	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:228878000-228882800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:228878000-228883200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:228878200-228883000	Strong transcription	Adipose Nuclei	Adipose
22	chr1:228878200-228883000	Strong transcription	Aorta	Aorta
23	chr1:228878600-228883000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:228878800-228883000	Strong transcription	Fetal Lung	lung
25	chr1:228878800-228883400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:228879200-228889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:228879400-228883800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:228880200-228882800	Strong transcription	Brain Substantia Nigra	brain
29	chr1:228880200-228883000	Genic enhancers	Fetal Thymus	thymus
30	chr1:228880400-228884200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:228880400-228885400	Weak transcription	A549	lung
32	chr1:228880400-228889400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:228880600-228883000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:228880600-228883800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:228880600-228889400	Weak transcription	Brain Anterior Caudate	brain
36	chr1:228880600-228889600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:228880600-228889600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:228880600-228890400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:228880800-228883400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:228880800-228884000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:228881000-228882800	Strong transcription	Brain Hippocampus Middle	brain
42	chr1:228881000-228882800	Weak transcription	Colonic Mucosa	Colon
43	chr1:228881000-228883200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:228881000-228883800	Weak transcription	Left Ventricle	heart
45	chr1:228881000-228884000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:228881000-228884200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:228881000-228884800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:228881000-228886600	Weak transcription	Gastric	stomach
49	chr1:228881000-228886800	Weak transcription	HepG2	liver
50	chr1:228881000-228889200	Weak transcription	Rectal Smooth Muscle	rectum

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