Variant report

Variant	rs12405174
Chromosome Location	chr1:228351768-228351769
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228350764-228354251	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:228351608-228352093	K562	blood:	n/a	n/a
3	POLR2A	chr1:228351494-228351928	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:228351371-228354514	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:228350272-228354541	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:228349082-228351793	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:228348937-228354538	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:228349847-228354537	MCF10A-Er-Src	breast:	n/a	n/a
9	TFAP2A	chr1:228350071-228351899	Hela-S3	cervix:	n/a	chr1:228350324-228350338 chr1:228350943-228350954 chr1:228351337-228351349 chr1:228350755-228350763 chr1:228350943-228350954 chr1:228351337-228351349 chr1:228350755-228350763 chr1:228351337-228351349 chr1:228350942-228350957 chr1:228350944-228350952 chr1:228350944-228350952 chr1:228350324-228350338 chr1:228350755-228350763 chr1:228351337-228351351 chr1:228350324-228350338 chr1:228351337-228351349 chr1:228350944-228350952
10	POLR2A	chr1:228349182-228354536	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:228351455-228354172	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr1:228349204-228352644	Raji	blood:	n/a	n/a
13	POLR2A	chr1:228351628-228354510	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228288054..228293498-chr1:228351743..228355627,9	K562	blood:
2	chr1:228350414..228357594-chr1:228359448..228365919,31	MCF-7	breast:
3	chr1:228349528..228352253-chr1:228378425..228381248,2	MCF-7	breast:
4	chr1:228288384..228298705-chr1:228351640..228357240,26	K562	blood:
5	chr1:228351767..228353945-chr1:228395258..228397219,2	MCF-7	breast:
6	chr1:228268894..228271778-chr1:228351302..228354925,4	MCF-7	breast:
7	chr1:228295286..228298610-chr1:228351640..228355026,4	K562	blood:
8	chr1:228350980..228355955-chr1:228356979..228359321,5	MCF-7	breast:

Variant related genes	Relation type
IBA57	TF binding region
ENSG00000154358	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000162910	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12033588	1.00[EUR][1000 genomes]
rs7516358	1.00[EUR][1000 genomes]
rs875980	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
10	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
11	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
13	nsv873258	chr1:228334088-228359775	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
14	nsv873259	chr1:228334277-228359775	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
15	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
16	nsv873261	chr1:228338939-228359775	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
17	nsv873262	chr1:228340653-228371098	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
18	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
19	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

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228338200-228352400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:228339400-228352600	Weak transcription	Brain Anterior Caudate	brain
3	chr1:228343400-228352400	Weak transcription	A549	lung
4	chr1:228344200-228352200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:228348600-228352600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:228348600-228352800	Enhancers	Fetal Thymus	thymus
7	chr1:228348600-228352800	Enhancers	Lung	lung
8	chr1:228348800-228351800	Enhancers	Fetal Intestine Large	intestine
9	chr1:228349000-228352200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr1:228349000-228352800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:228349000-228352800	Enhancers	Placenta	Placenta
12	chr1:228349200-228352800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr1:228349200-228352800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:228349200-228352800	Enhancers	Pancreas	Pancrea
15	chr1:228349200-228352800	Enhancers	Right Ventricle	heart
16	chr1:228349200-228352800	Enhancers	HMEC	breast
17	chr1:228349200-228352800	Enhancers	HUVEC	blood vessel
18	chr1:228349400-228352600	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:228349600-228351800	Enhancers	Fetal Intestine Small	intestine
20	chr1:228349600-228352200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:228349600-228352800	Enhancers	Psoas Muscle	Psoas
22	chr1:228349600-228352800	Enhancers	Spleen	Spleen
23	chr1:228350000-228351800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:228350000-228351800	Flanking Active TSS	NHEK	skin
25	chr1:228350000-228352200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:228350200-228352800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:228350200-228352800	Flanking Active TSS	Hela-S3	cervix
28	chr1:228350400-228352000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:228350400-228352600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:228350400-228352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:228350400-228352800	Weak transcription	Brain Angular Gyrus	brain
32	chr1:228350400-228352800	Enhancers	Fetal Muscle Leg	muscle
33	chr1:228350400-228352800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:228350600-228352400	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:228350600-228352400	Weak transcription	Thymus	Thymus
36	chr1:228350600-228352600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:228350600-228352600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:228350600-228352600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:228350600-228352800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:228350600-228352800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:228350800-228351800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:228350800-228351800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr1:228350800-228352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:228350800-228352000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:228350800-228352000	Weak transcription	K562	blood
46	chr1:228350800-228352200	Weak transcription	Primary B cells from cord blood	blood
47	chr1:228350800-228352200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:228350800-228352200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:228350800-228352400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:228350800-228352400	Weak transcription	Fetal Lung	lung

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