Variant report

Variant	rs4653951
Chromosome Location	chr1:228579788-228579789
allele	C/T
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	MAX	chr1:228579655-228580276	NB4	blood:	n/a	chr1:228580025-228580034 chr1:228580026-228580035
2	POLR2A	chr1:228578921-228580568	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:228578293-228588731	K562	blood:	n/a	n/a
4	POLR2A	chr1:228579227-228580304	U87	brain:	n/a	n/a
5	POLR2A	chr1:228579748-228579931	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:228579756-228579968	U87	brain:	n/a	n/a
7	MAX	chr1:228579755-228580171	K562	blood:	n/a	chr1:228580025-228580034 chr1:228580026-228580035
8	POLR2A	chr1:228579456-228579824	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:228579022-228584149	K562	blood:	n/a	n/a
10	POLR2A	chr1:228578971-228580271	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:228579236-228580249	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:228579516-228580327	HCT-116	colon:	n/a	n/a
13	POLR2A	chr1:228578861-228580600	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr1:228579221-228580285	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:228579239-228580211	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr1:228579525-228579935	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:228579027-228580641	K562	blood:	n/a	n/a
18	POLR2A	chr1:228579004-228580070	GM19193	blood:	n/a	n/a
19	POLR2A	chr1:228578911-228580249	K562	blood:	n/a	n/a
20	POLR2A	chr1:228579434-228580181	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:228579479-228580091	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:228579376-228580019	ProgFib	skin:	n/a	n/a
23	POLR2A	chr1:228578889-228580539	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:228579425-228579907	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr1:228578983-228580529	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:228579548-228580073	HepG2	liver:	n/a	n/a
27	FOSL1	chr1:228579700-228580356	HCT-116	colon:	n/a	chr1:228580025-228580034 chr1:228580027-228580034 chr1:228580026-228580034
28	JUND	chr1:228579691-228580361	HCT-116	colon:	n/a	chr1:228580025-228580034 chr1:228580027-228580034 chr1:228580024-228580035 chr1:228580026-228580034
29	POLR2A	chr1:228579758-228579894	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr1:228578885-228582513	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr1:228579048-228580260	GM12892	blood:	n/a	n/a
32	POLR2A	chr1:228579781-228580277	HCT-116	colon:	n/a	n/a
33	TEAD4	chr1:228579537-228580183	K562	blood:	n/a	n/a
34	POLR2A	chr1:228579429-228580563	K562	blood:	n/a	n/a
35	POLR2A	chr1:228579075-228579949	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:228579666-228580215	SK-N-MC	brain:	n/a	n/a
37	BCL3	chr1:228579407-228580047	A549	lung:	n/a	chr1:228580026-228580035 chr1:228580025-228580034
38	POLR2A	chr1:228579010-228580263	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:228578913-228580349	MCF-7	breast:	n/a	n/a
40	POLR2A	chr1:228579675-228580220	K562	blood:	n/a	n/a
41	TBL1XR1	chr1:228579739-228580062	K562	blood:	n/a	n/a
42	POLR2A	chr1:228578930-228580109	GM12891	blood:	n/a	n/a
43	POLR2A	chr1:228578970-228580365	A549	lung:	n/a	n/a
44	POLR2A	chr1:228579766-228580181	H1-hESC	embryonic stem cell:	n/a	n/a
45	JUN	chr1:228579767-228580180	K562	blood:	n/a	chr1:228580025-228580034 chr1:228580027-228580034 chr1:228580026-228580034
46	POLR2A	chr1:228579221-228580304	U87	brain:	n/a	n/a
47	POLR2A	chr1:228578956-228580579	HL-60	blood:	n/a	n/a
48	POLR2A	chr1:228579574-228580128	GM12891	blood:	n/a	n/a
49	POLR2A	chr1:228579415-228580073	GM12892	blood:	n/a	n/a
50	MYC	chr1:228579775-228580271	NB4	blood:	n/a	chr1:228580025-228580034 chr1:228580026-228580035

No.	Distal block	Cell Line	Cell type
1	chr1:228576966..228583255-chr1:228642395..228646960,7	MCF-7	breast:
2	chr1:228565600..228567637-chr1:228578632..228580463,2	MCF-7	breast:
3	chr1:228579742..228582257-chr1:228643966..228647332,3	MCF-7	breast:
4	chr1:228579319..228581517-chr1:228584459..228586560,2	MCF-7	breast:
5	chr1:228461221..228463788-chr1:228578693..228581297,2	K562	blood:
6	chr1:228577984..228580608-chr1:228681931..228684141,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270094	TF binding region
ENSG00000269890	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000181218	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12080246	1.00[YRI][hapmap]
rs17640616	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3795809	1.00[CHB][hapmap]
rs4653943	1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 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	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
5	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
6	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv873274	chr1:228450868-228585837	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv873275	chr1:228456147-228585837	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
12	nsv873276	chr1:228456943-228585837	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
14	nsv873278	chr1:228464248-228585837	Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv468271	chr1:228464248-228601638	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv468283	chr1:228464248-228601638	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv468294	chr1:228464248-228601638	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
18	nsv549295	chr1:228464248-228601638	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	nsv470780	chr1:228464248-228606965	Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
21	nsv873280	chr1:228500627-228603029	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
23	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
24	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
25	nsv508697	chr1:228540037-228622614	Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228566800-228583200	Weak transcription	HSMMtube	muscle
2	chr1:228567000-228579800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:228567000-228592800	Weak transcription	Fetal Kidney	kidney
4	chr1:228567200-228581600	Weak transcription	Right Ventricle	heart
5	chr1:228567400-228579800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:228567400-228582200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:228567600-228582600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:228568200-228582800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:228569200-228582000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:228569800-228585600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:228571000-228591600	Weak transcription	Fetal Brain Male	brain
12	chr1:228571600-228582600	Weak transcription	Small Intestine	intestine
13	chr1:228573600-228582000	Weak transcription	Ovary	ovary
14	chr1:228573800-228580000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:228573800-228583800	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:228574000-228581200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:228574200-228579800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:228574800-228581000	Weak transcription	NHEK	skin
19	chr1:228575000-228579800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:228575200-228580000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:228575400-228579800	Weak transcription	NHLF	lung
22	chr1:228575600-228582200	Weak transcription	Left Ventricle	heart
23	chr1:228576200-228579800	Weak transcription	Fetal Thymus	thymus
24	chr1:228576200-228580200	Weak transcription	Adipose Nuclei	Adipose
25	chr1:228576400-228579800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:228576400-228582200	Weak transcription	Aorta	Aorta
27	chr1:228576600-228579800	Weak transcription	Brain Germinal Matrix	brain
28	chr1:228576600-228580000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:228576600-228583600	Weak transcription	Brain Angular Gyrus	brain
30	chr1:228576800-228579800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:228576800-228579800	Weak transcription	Esophagus	oesophagus
32	chr1:228576800-228580000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:228576800-228582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:228577000-228579800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:228577000-228580800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:228577000-228580800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:228577000-228582600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:228577000-228592600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:228577200-228579800	Weak transcription	Primary B cells from cord blood	blood
40	chr1:228577400-228579800	Weak transcription	Primary T cells from cord blood	blood
41	chr1:228577400-228579800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:228577400-228579800	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:228577400-228580000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:228577400-228580000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:228577400-228580400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:228577400-228581800	Weak transcription	Fetal Intestine Large	intestine
47	chr1:228577400-228582800	Weak transcription	HMEC	breast
48	chr1:228577400-228590800	Weak transcription	Right Atrium	heart
49	chr1:228577600-228580000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:228577600-228580000	Weak transcription	Stomach Smooth Muscle	stomach

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