Variant report

Variant	rs28519439
Chromosome Location	chr7:140085009-140085010
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	EP300	chr7:140084695-140085129	SK-N-SH_RA	brain:	n/a	n/a
2	POLR2A	chr7:140084805-140085321	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140082007..140083740-chr7:140084020..140086777,2	K562	blood:
2	chr7:140081489..140083919-chr7:140084216..140086210,2	MCF-7	breast:

Variant related genes	Relation type
SLC37A3	TF binding region
ENSG00000157800	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10281239	1.00[EUR][1000 genomes]
rs11764502	0.89[EUR][1000 genomes]
rs11771118	0.89[EUR][1000 genomes]
rs11773100	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34595563	0.85[ASN][1000 genomes]
rs3924960	1.00[EUR][1000 genomes]
rs59072471	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60864294	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6464705	0.89[EUR][1000 genomes]
rs6943032	0.93[EUR][1000 genomes]
rs6947516	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6955063	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6962376	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6964259	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6966078	1.00[EUR][1000 genomes]
rs6976631	1.00[EUR][1000 genomes]
rs6978245	0.90[EUR][1000 genomes]
rs73472784	0.89[EUR][1000 genomes]
rs73472791	0.89[EUR][1000 genomes]
rs7777468	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7784544	0.82[EUR][1000 genomes]
rs7788727	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7789964	0.89[EUR][1000 genomes]
rs7806111	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9640465	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140033600-140096000	Weak transcription	Stomach Mucosa	stomach
2	chr7:140034800-140085600	Weak transcription	Psoas Muscle	Psoas
3	chr7:140049200-140090200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:140058600-140096000	Weak transcription	Small Intestine	intestine
6	chr7:140058800-140097200	Weak transcription	Brain Anterior Caudate	brain
7	chr7:140059400-140091400	Weak transcription	Fetal Heart	heart
8	chr7:140068000-140089000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:140069600-140091800	Weak transcription	Esophagus	oesophagus
10	chr7:140076400-140088800	Weak transcription	GM12878-XiMat	blood
11	chr7:140076600-140090000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:140076600-140090200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr7:140076800-140089600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:140076800-140089600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:140076800-140096200	Weak transcription	NHLF	lung
16	chr7:140078200-140090000	Weak transcription	Pancreas	Pancrea
17	chr7:140080200-140085400	Weak transcription	Brain Substantia Nigra	brain
18	chr7:140080200-140089400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:140080200-140089800	Weak transcription	HSMM	muscle
20	chr7:140080200-140090200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:140080200-140090200	Weak transcription	HMEC	breast
22	chr7:140080200-140095800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr7:140080200-140096000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:140080200-140097200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:140080200-140097200	Weak transcription	HSMMtube	muscle
26	chr7:140080200-140097600	Weak transcription	Brain Angular Gyrus	brain
27	chr7:140080600-140088800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr7:140080600-140089000	Weak transcription	Spleen	Spleen
29	chr7:140080600-140089600	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:140080600-140089800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:140080600-140090000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:140080600-140090200	Weak transcription	Primary T cells from cord blood	blood
33	chr7:140080600-140090400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:140080600-140096200	Weak transcription	HepG2	liver
35	chr7:140080600-140097400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr7:140080800-140085200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:140080800-140089800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:140080800-140090600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr7:140080800-140096200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr7:140081400-140097200	Weak transcription	Brain Germinal Matrix	brain
41	chr7:140081600-140089200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:140081800-140093000	Weak transcription	Fetal Intestine Small	intestine
43	chr7:140082000-140089600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:140082200-140088800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:140082200-140089800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:140082200-140090200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr7:140082200-140090200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:140082200-140090200	Weak transcription	NH-A	brain
49	chr7:140082200-140093000	Weak transcription	Fetal Stomach	stomach
50	chr7:140082200-140096200	Weak transcription	Fetal Lung	lung

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