Variant report

Variant	rs10234020
Chromosome Location	chr7:21984590-21984591
allele	G/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	chr7:21984214-21984597	HCT-116	colon:	n/a	n/a
2	STAT1	chr7:21984258-21986326	Hela-S3	cervix:	n/a	chr7:21985026-21985037
3	RELA	chr7:21984420-21985971	GM15510	blood:	n/a	n/a
4	TBP	chr7:21984238-21984609	H1-hESC	embryonic stem cell:	n/a	n/a
5	TBP	chr7:21984287-21986247	Hela-S3	cervix:	n/a	n/a
6	CHD2	chr7:21984221-21986258	Hela-S3	cervix:	n/a	chr7:21985502-21985512
7	POLR2A	chr7:21984271-21984630	HL-60	blood:	n/a	n/a
8	TAF1	chr7:21984281-21984644	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD2	chr7:21984318-21986229	H1-hESC	embryonic stem cell:	n/a	chr7:21985502-21985512
10	MYC	chr7:21984247-21986220	NB4	blood:	n/a	chr7:21984693-21984701
11	POLR2A	chr7:21984156-21986103	HL-60	blood:	n/a	n/a
12	MAX	chr7:21984266-21986319	Hela-S3	cervix:	n/a	chr7:21984693-21984701
13	MYC	chr7:21984346-21986193	MCF10A-Er-Src	breast:	n/a	chr7:21984693-21984701
14	RCOR1	chr7:21984299-21985874	GM12878	blood:	n/a	n/a
15	MYC	chr7:21984333-21986293	Hela-S3	cervix:	n/a	chr7:21984693-21984701
16	BRCA1	chr7:21984317-21986193	Hela-S3	cervix:	n/a	n/a
17	KAP1	chr7:21984216-21986180	HEK293	kidney:	n/a	n/a
18	MTA3	chr7:21984167-21986093	GM12878	blood:	n/a	n/a
19	ELK4	chr7:21984328-21984938	Hela-S3	cervix:	n/a	n/a
20	MAZ	chr7:21984260-21986001	GM12878	blood:	n/a	chr7:21984693-21984701
21	GTF2F1	chr7:21984391-21986314	Hela-S3	cervix:	n/a	n/a
22	MAX	chr7:21984163-21984739	ECC-1	luminal epithelium:	n/a	chr7:21984693-21984701
23	TCF12	chr7:21984231-21984739	ECC-1	luminal epithelium:	n/a	chr7:21984623-21984632
24	POLR2A	chr7:21984331-21984597	Hela-S3	cervix:	n/a	n/a
25	FOXA2	chr7:21984225-21984683	A549	lung:	n/a	n/a
26	HA-E2F1	chr7:21984053-21986311	MCF-7	breast:	n/a	chr7:21985238-21985252 chr7:21985091-21985100 chr7:21984387-21984396 chr7:21985241-21985255 chr7:21985675-21985685 chr7:21985375-21985384
27	ZNF263	chr7:21984142-21986149	HEK293-T-REx	kidney:	n/a	n/a
28	FOXA1	chr7:21984290-21984640	HepG2	liver:	n/a	chr7:21984426-21984441
29	PML	chr7:21984474-21986133	GM12878	blood:	n/a	n/a
30	JUND	chr7:21984510-21986177	H1-hESC	embryonic stem cell:	n/a	chr7:21985475-21985483 chr7:21985378-21985387
31	POLR2A	chr7:21984175-21984903	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr7:21984291-21986183	GM18505	blood:	n/a	n/a
33	POLR2A	chr7:21984148-21984857	H1-hESC	embryonic stem cell:	n/a	n/a
34	NFIC	chr7:21984357-21986004	GM12878	blood:	n/a	n/a
35	POLR2A	chr7:21984207-21986270	Hela-S3	cervix:	n/a	n/a
36	FOXA1	chr7:21984262-21984621	HepG2	liver:	n/a	chr7:21984426-21984441
37	TBL1XR1	chr7:21984291-21986086	GM12878	blood:	n/a	n/a
38	CTCF	chr7:21984280-21984617	GM12878	blood:	n/a	n/a
39	SIN3A	chr7:21984140-21986096	H1-hESC	embryonic stem cell:	n/a	chr7:21985744-21985755 chr7:21985806-21985819 chr7:21985266-21985277 chr7:21985093-21985102 chr7:21985236-21985247
40	CHD1	chr7:21984059-21986341	H1-hESC	embryonic stem cell:	n/a	chr7:21985502-21985512
41	RCOR1	chr7:21984261-21986332	Hela-S3	cervix:	n/a	n/a
42	MYC	chr7:21984297-21984612	H1-hESC	embryonic stem cell:	n/a	n/a
43	EP300	chr7:21984515-21986053	GM12878	blood:	n/a	chr7:21985504-21985520 chr7:21985227-21985243 chr7:21985093-21985109 chr7:21984622-21984632 chr7:21985545-21985554 chr7:21985374-21985390 chr7:21985545-21985561 chr7:21985739-21985755
44	MAX	chr7:21984157-21984732	HCT-116	colon:	n/a	chr7:21984693-21984701
45	BHLHE40	chr7:21984123-21986080	GM12878	blood:	n/a	chr7:21985817-21985833 chr7:21985374-21985390
46	MXI1	chr7:21984270-21986170	IMR90	lung:	n/a	n/a
47	MAX	chr7:21984102-21984725	A549	lung:	n/a	chr7:21984693-21984701
48	MAX	chr7:21984246-21984619	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr7:21984175-21986315	GM12891	blood:	n/a	n/a
50	TAF1	chr7:21984196-21984612	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:65588158..65588861-chr7:21984144..21985018,2	Hela-S3	cervix:
2	chr7:21984509..21985113-chr7:27779779..27780555,2	Hela-S3	cervix:
3	chr5:179126005..179126615-chr7:21984529..21985309,2	Hela-S3	cervix:
4	chr1:155880615..155881579-chr7:21984391..21985346,2	Hela-S3	cervix:

Variant related genes	Relation type
CDCA7L	TF binding region
ENSG00000229893	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000106052	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000143622	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10238000	0.85[AMR][1000 genomes]
rs10254992	0.80[AFR][1000 genomes]
rs10258599	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10261926	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10263850	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28640950	0.80[AFR][1000 genomes]
rs6944457	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv870325	chr7:21979039-22120493	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21982800-21985800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:21983000-21984800	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr7:21983200-21984600	Weak transcription	Gastric	stomach
4	chr7:21983200-21985800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr7:21983200-21985800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:21983400-21986000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:21983600-21985400	Active TSS	Stomach Smooth Muscle	stomach
8	chr7:21983600-21985800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr7:21983600-21985800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:21983600-21986000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr7:21983600-21986000	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr7:21983600-21986000	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr7:21983600-21986000	Active TSS	Ovary	ovary
14	chr7:21983600-21986000	Active TSS	Right Ventricle	heart
15	chr7:21983600-21986200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr7:21983600-21986200	Active TSS	NHDF-Ad	bronchial
17	chr7:21983800-21985200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:21983800-21985400	Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr7:21983800-21985400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:21983800-21985400	Active TSS	Fetal Heart	heart
21	chr7:21983800-21985600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:21983800-21985600	Active TSS	Thymus	Thymus
23	chr7:21983800-21985800	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr7:21983800-21985800	Active TSS	GM12878-XiMat	blood
25	chr7:21983800-21985800	Active TSS	NHEK	skin
26	chr7:21983800-21986000	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr7:21983800-21986000	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr7:21983800-21986000	Active TSS	Colon Smooth Muscle	Colon
29	chr7:21984000-21984600	Flanking Active TSS	Liver	Liver
30	chr7:21984000-21984600	Active TSS	Duodenum Mucosa	Duodenum
31	chr7:21984000-21984600	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr7:21984000-21984600	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr7:21984000-21985000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr7:21984000-21985000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr7:21984000-21985000	Flanking Active TSS	NH-A	brain
36	chr7:21984000-21985000	Flanking Active TSS	Osteobl	bone
37	chr7:21984000-21985400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr7:21984000-21985400	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr7:21984000-21985600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:21984000-21985600	Active TSS	Fetal Intestine Small	intestine
41	chr7:21984000-21985600	Active TSS	Fetal Stomach	stomach
42	chr7:21984000-21985800	Active TSS	H1 Cell Line	embryonic stem cell
43	chr7:21984000-21985800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:21984000-21985800	Active TSS	Fetal Lung	lung
45	chr7:21984000-21985800	Active TSS	HSMMtube	muscle
46	chr7:21984000-21985800	Active TSS	NHLF	lung
47	chr7:21984000-21986000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:21984000-21986000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr7:21984000-21986000	Active TSS	Fetal Kidney	kidney
50	chr7:21984000-21986000	Active TSS	Right Atrium	heart

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