Variant report

Variant	rs56267204
Chromosome Location	chr17:19995330-19995331
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	POLR2A	chr17:19994916-19995402	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr17:19994929-19995508	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19894457..19896275-chr17:19994382..19996657,2	MCF-7	breast:
2	chr17:19980057..19981963-chr17:19993152..19995446,2	K562	blood:
3	chr17:19994190..19996745-chr17:20058300..20060298,2	MCF-7	breast:

Variant related genes	Relation type
SPECC1	TF binding region
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs16960662	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16960672	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55650639	0.81[EUR][1000 genomes]
rs55814709	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55832890	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55853482	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55854412	0.89[EUR][1000 genomes]
rs55891925	0.85[EUR][1000 genomes]
rs55939726	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56002404	0.85[EUR][1000 genomes]
rs56009494	0.89[EUR][1000 genomes]
rs56009515	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56020655	0.81[EUR][1000 genomes]
rs56034568	0.91[EUR][1000 genomes]
rs56074205	0.85[EUR][1000 genomes]
rs56186136	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56194672	0.89[EUR][1000 genomes]
rs56208903	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56281769	0.89[EUR][1000 genomes]
rs56301435	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56344048	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7207672	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72830109	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72830114	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72830123	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72830128	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830139	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72830140	0.80[EUR][1000 genomes]
rs72830141	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72830145	0.89[EUR][1000 genomes]
rs72830150	0.84[EUR][1000 genomes]
rs72830153	0.89[EUR][1000 genomes]
rs72830165	0.89[EUR][1000 genomes]
rs72830176	0.89[EUR][1000 genomes]
rs72830177	0.87[EUR][1000 genomes]
rs72830178	0.89[EUR][1000 genomes]
rs72830179	0.85[EUR][1000 genomes]
rs72830188	0.85[EUR][1000 genomes]
rs72830191	0.81[EUR][1000 genomes]
rs72830194	0.81[EUR][1000 genomes]
rs72830197	0.81[EUR][1000 genomes]
rs72830202	0.81[EUR][1000 genomes]
rs72832504	0.81[EUR][1000 genomes]
rs72832508	0.81[EUR][1000 genomes]
rs72832515	0.81[EUR][1000 genomes]
rs72832518	0.81[EUR][1000 genomes]
rs72832520	0.81[EUR][1000 genomes]
rs72832522	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh 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
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv2762522	chr17:19976462-19996429	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:19990000-19995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:19990200-19998800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:19991200-19996800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr17:19992600-19995400	Weak transcription	Aorta	Aorta
6	chr17:19993000-19996800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr17:19993200-19996600	Enhancers	Fetal Muscle Leg	muscle
8	chr17:19993400-20006400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:19993600-19996000	Enhancers	NHDF-Ad	bronchial
10	chr17:19993600-19998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:19993600-20000000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr17:19993600-20003600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:19993800-19995800	Weak transcription	Left Ventricle	heart
14	chr17:19993800-19996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:19993800-19998600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:19993800-19998800	Weak transcription	Spleen	Spleen
17	chr17:19993800-20000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:19993800-20001600	Weak transcription	Lung	lung
19	chr17:19993800-20006400	Weak transcription	Esophagus	oesophagus
20	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
21	chr17:19994000-19996200	Enhancers	NH-A	brain
22	chr17:19994000-19996800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr17:19994000-19997800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr17:19994400-19996000	Enhancers	Fetal Muscle Trunk	muscle
25	chr17:19994400-19996800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr17:19994600-19995400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:19994600-19995400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr17:19994600-19995400	Flanking Active TSS	Osteobl	bone
29	chr17:19994600-19995600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr17:19994600-19995600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:19994600-19995600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:19994600-19995600	Enhancers	Fetal Stomach	stomach
33	chr17:19994600-19995800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:19994600-19996400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr17:19994600-19996800	Enhancers	H9 Cell Line	embryonic stem cell
36	chr17:19994600-19997000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr17:19994600-19997000	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr17:19994600-19997000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr17:19994600-19997000	Enhancers	Brain Cingulate Gyrus	brain
40	chr17:19994600-19997200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:19994600-19997200	Enhancers	Brain Anterior Caudate	brain
42	chr17:19994600-19998400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:19994600-19998600	Enhancers	Brain Hippocampus Middle	brain
44	chr17:19994800-19995400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr17:19994800-19996800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr17:19994800-19996800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr17:19994800-19997200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr17:19995000-19995400	Weak transcription	Brain Angular Gyrus	brain
49	chr17:19995000-19995600	Weak transcription	Psoas Muscle	Psoas
50	chr17:19995000-19996000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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