Variant report

Variant	rs7554146
Chromosome Location	chr1:147016629-147016630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:147014865..147017655-chr1:147069985..147072469,3	MCF-7	breast:
2	chr1:147015861..147018726-chr1:147069919..147072296,3	MCF-7	breast:
3	chr1:147004459..147006427-chr1:147014371..147016886,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116128	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1027424	0.81[ASW][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs10494254	1.00[MEX][hapmap]
rs11240032	1.00[MEX][hapmap]
rs11240079	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12069005	1.00[EUR][1000 genomes]
rs12072533	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075087	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12085860	1.00[MEX][hapmap]
rs17160340	0.96[EUR][1000 genomes]
rs1989733	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57710974	1.00[EUR][1000 genomes]
rs58718844	1.00[EUR][1000 genomes]
rs59594924	1.00[EUR][1000 genomes]
rs6668185	0.82[EUR][1000 genomes]
rs716703	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs74125727	1.00[EUR][1000 genomes]
rs7526630	0.96[EUR][1000 genomes]
rs7526706	1.00[EUR][1000 genomes]
rs7535258	1.00[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
3	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers 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 target site	110 gene(s)	inside rSNPs	diseases
4	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	113 gene(s)	inside rSNPs	diseases
6	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS 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	111 gene(s)	inside rSNPs	diseases
7	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	111 gene(s)	inside rSNPs	diseases
8	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
9	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
15	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	49 gene(s)	inside rSNPs	diseases
16	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS 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 miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv534063	chr1:146807433-147381411	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
19	nsv831414	chr1:146884994-147083866	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv1001868	chr1:146893791-147389944	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
21	nsv482606	chr1:146959127-147134517	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
22	nsv946308	chr1:147013512-147039086	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:147013400-147017600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr1:147014000-147017600	Enhancers	Dnd41	blood
3	chr1:147014200-147016800	Weak transcription	HSMM	muscle
4	chr1:147014400-147016800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:147014400-147016800	Weak transcription	Hela-S3	cervix
6	chr1:147014400-147017000	Weak transcription	Gastric	stomach
7	chr1:147014400-147017200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:147014400-147017800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:147014400-147018400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:147014400-147018400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:147014400-147018800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:147014400-147020200	Weak transcription	Esophagus	oesophagus
13	chr1:147014600-147016800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:147014600-147016800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:147014600-147016800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:147014600-147016800	Weak transcription	Right Ventricle	heart
17	chr1:147014600-147016800	Weak transcription	Small Intestine	intestine
18	chr1:147014600-147017000	Enhancers	H9 Cell Line	embryonic stem cell
19	chr1:147014600-147017600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:147014600-147018000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:147014600-147018800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:147014800-147017000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:147014800-147017000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:147014800-147017000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:147014800-147017200	Enhancers	Brain Hippocampus Middle	brain
26	chr1:147014800-147017400	Flanking Active TSS	Fetal Brain Female	brain
27	chr1:147014800-147017400	Enhancers	Fetal Heart	heart
28	chr1:147014800-147018600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr1:147015000-147017000	Weak transcription	NHLF	lung
30	chr1:147015000-147018400	Enhancers	Fetal Thymus	thymus
31	chr1:147015000-147021800	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:147015200-147016800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:147015200-147016800	Weak transcription	NH-A	brain
34	chr1:147015200-147017000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:147015200-147017000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:147015200-147017400	Enhancers	Fetal Intestine Large	intestine
37	chr1:147015200-147017400	Enhancers	Fetal Intestine Small	intestine
38	chr1:147015200-147017800	Enhancers	Colon Smooth Muscle	Colon
39	chr1:147015200-147032200	Weak transcription	Brain Angular Gyrus	brain
40	chr1:147015400-147017600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:147015600-147016800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:147015600-147017200	Enhancers	Psoas Muscle	Psoas
43	chr1:147015600-147017200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:147015600-147017800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:147015600-147018000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:147015600-147018000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:147015800-147017000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:147015800-147017000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:147015800-147017400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:147015800-147017400	Enhancers	Fetal Lung	lung

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