Variant report

Variant	rs74092338
Chromosome Location	chr1:78421503-78421504
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	chr1:78419417-78421875	K562	blood:	n/a	n/a
2	POLR2A	chr1:78421351-78421713	K562	blood:	n/a	n/a
3	POLR2A	chr1:78419137-78428700	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:78421358-78421713	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:78421493-78421627	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:78420965-78421606	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:78421012-78421547	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78419725..78422750-chr1:78442650..78445885,3	MCF-7	breast:

Variant related genes	Relation type
FUBP1	TF binding region
ENSG00000137960	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000162613	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17098321	1.00[EUR][1000 genomes]
rs17101286	1.00[EUR][1000 genomes]
rs17101443	1.00[EUR][1000 genomes]
rs55717739	1.00[EUR][1000 genomes]
rs56010524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58120905	1.00[EUR][1000 genomes]
rs60000721	1.00[EUR][1000 genomes]
rs60658102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74090686	1.00[EUR][1000 genomes]
rs74092304	1.00[EUR][1000 genomes]
rs74092305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74092316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74092323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74092325	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74092336	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74092337	1.00[EUR][1000 genomes]
rs74092342	1.00[EUR][1000 genomes]
rs74092352	1.00[EUR][1000 genomes]
rs74092353	1.00[AMR][1000 genomes];1.00[EUR][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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 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	chr1:78405800-78432200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:78405800-78442200	Strong transcription	Fetal Thymus	thymus
3	chr1:78406000-78426600	Weak transcription	Fetal Heart	heart
4	chr1:78406000-78436200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:78406600-78436200	Strong transcription	Liver	Liver
6	chr1:78406600-78440600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:78406800-78436400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:78407000-78434400	Strong transcription	Dnd41	blood
9	chr1:78407000-78437200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:78407400-78427600	Strong transcription	Fetal Intestine Large	intestine
11	chr1:78407400-78432800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:78407400-78436600	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr1:78407400-78437600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:78407400-78437800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr1:78407600-78435400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:78407600-78435600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:78407600-78437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:78407800-78435400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:78407800-78436800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr1:78407800-78437200	Strong transcription	Placenta	Placenta
21	chr1:78408000-78437600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:78408200-78434200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:78408400-78436400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:78408400-78439600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:78408600-78437000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:78409600-78432000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:78409600-78432200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:78409600-78437200	Strong transcription	Hela-S3	cervix
29	chr1:78410000-78433800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:78410600-78427400	Strong transcription	HepG2	liver
31	chr1:78411800-78438200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:78412400-78434800	Strong transcription	Fetal Lung	lung
33	chr1:78412800-78434800	Strong transcription	Fetal Brain Female	brain
34	chr1:78413000-78423000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:78413000-78432600	Strong transcription	Primary T cells from cord blood	blood
36	chr1:78415000-78434200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:78415000-78435800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:78415000-78437200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:78415200-78427200	Strong transcription	NH-A	brain
40	chr1:78415200-78430600	Strong transcription	Brain Cingulate Gyrus	brain
41	chr1:78415600-78424000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:78415600-78434800	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr1:78415800-78421600	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr1:78415800-78422200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:78415800-78423400	Strong transcription	Fetal Kidney	kidney
46	chr1:78415800-78432400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:78415800-78434800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:78415800-78435200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:78415800-78436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:78415800-78436800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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