Variant report

Variant	rs2254083
Chromosome Location	chr6:31639741-31639742
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	chr6:31638089-31640209	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:31639445-31640049	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr6:31639525-31640114	HL-60	blood:	n/a	n/a
4	POLR2A	chr6:31639504-31639993	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:31636602-31640237	K562	blood:	n/a	n/a
6	POLR2A	chr6:31639693-31640207	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:31638021-31640115	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:31637810-31640233	K562	blood:	n/a	n/a
9	POLR2A	chr6:31639346-31640326	K562	blood:	n/a	n/a
10	POLR2A	chr6:31637892-31640307	K562	blood:	n/a	n/a
11	POLR2A	chr6:31639521-31640203	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:31514014..31516004-chr6:31637492..31640233,2	MCF-7	breast:

Variant related genes	Relation type
LY6G5B	TF binding region
ENSG00000204498	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000213760	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11961829	0.91[AFR][1000 genomes]
rs11964779	1.00[EUR][1000 genomes]
rs11965323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966331	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11967206	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2295666	1.00[ASN][1000 genomes]
rs2295667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28399971	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34453162	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713482	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4947252	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4947329	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947330	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59002496	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59114240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60149397	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60559550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60900316	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73398259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398298	0.91[AFR][1000 genomes]
rs7382084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9800604	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking 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 miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
15	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31634200-31640000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:31634600-31639800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:31634800-31641400	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr6:31634800-31641400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:31634800-31641400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:31634800-31641400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:31634800-31648200	Weak transcription	Right Atrium	heart
8	chr6:31635000-31640200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:31635000-31640800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:31635000-31641400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:31635000-31641400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:31635000-31641400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:31635000-31641400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:31635000-31641400	Strong transcription	Brain Cingulate Gyrus	brain
15	chr6:31635000-31641800	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:31635000-31641800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr6:31635000-31642000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:31635000-31642000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:31635000-31642000	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr6:31635000-31642000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:31635000-31642000	Strong transcription	Spleen	Spleen
22	chr6:31635000-31642200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr6:31635000-31642800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:31635000-31642800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:31635000-31643800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:31635200-31639800	Strong transcription	Fetal Brain Male	brain
27	chr6:31635200-31640200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:31635200-31640200	Strong transcription	HUVEC	blood vessel
29	chr6:31635200-31640800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:31635200-31641200	Strong transcription	Esophagus	oesophagus
31	chr6:31635200-31641200	Strong transcription	Fetal Lung	lung
32	chr6:31635200-31641400	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr6:31635200-31641400	Strong transcription	Colonic Mucosa	Colon
34	chr6:31635200-31641600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:31635200-31641800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:31635200-31641800	Strong transcription	HSMMtube	muscle
37	chr6:31635200-31642000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:31635200-31642200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:31635200-31643600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr6:31635400-31639800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr6:31635400-31640400	Strong transcription	NHDF-Ad	bronchial
42	chr6:31635400-31640800	Strong transcription	HMEC	breast
43	chr6:31635400-31641200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:31635400-31641400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:31635400-31641400	Strong transcription	Brain Angular Gyrus	brain
46	chr6:31635400-31641400	Strong transcription	Ovary	ovary
47	chr6:31635400-31641400	Strong transcription	Right Ventricle	heart
48	chr6:31635400-31641600	Strong transcription	Fetal Brain Female	brain
49	chr6:31635400-31642000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:31635400-31642000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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