Variant report

Variant	rs10238000
Chromosome Location	chr7:21985383-21985384
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	STAT1	chr7:21984258-21986326	Hela-S3	cervix:	n/a	chr7:21985026-21985037
2	EP300	chr7:21985247-21986051	T-47D	breast:	n/a	chr7:21985504-21985520 chr7:21985545-21985554 chr7:21985374-21985390 chr7:21985545-21985561 chr7:21985739-21985755
3	EP300	chr7:21985361-21985778	GM12878	blood:	n/a	chr7:21985504-21985520 chr7:21985545-21985554 chr7:21985374-21985390 chr7:21985545-21985561 chr7:21985739-21985755
4	POU2F2	chr7:21984983-21985655	GM12891	blood:	n/a	chr7:21985116-21985128
5	POLR2A	chr7:21984952-21985599	ECC-1	luminal epithelium:	n/a	n/a
6	RAD21	chr7:21985004-21985493	ECC-1	luminal epithelium:	n/a	chr7:21985128-21985141
7	RELA	chr7:21984420-21985971	GM15510	blood:	n/a	n/a
8	ZBTB7A	chr7:21984938-21985938	ECC-1	luminal epithelium:	n/a	n/a
9	SIN3AK20	chr7:21984853-21985983	PANC-1	pancreas:	n/a	n/a
10	RAD21	chr7:21985113-21985452	H1-hESC	embryonic stem cell:	n/a	chr7:21985128-21985141
11	NRF1	chr7:21985082-21986117	GM12878	blood:	n/a	chr7:21985504-21985513 chr7:21985116-21985125
12	TBP	chr7:21984287-21986247	Hela-S3	cervix:	n/a	n/a
13	FOXM1	chr7:21984888-21986072	GM12878	blood:	n/a	n/a
14	CHD2	chr7:21984221-21986258	Hela-S3	cervix:	n/a	chr7:21985502-21985512
15	POLR2A	chr7:21984829-21986213	U87	brain:	n/a	n/a
16	SP1	chr7:21985119-21986139	A549	lung:	n/a	chr7:21985970-21985979 chr7:21986122-21986132
17	E2F6	chr7:21985062-21986072	H1-hESC	embryonic stem cell:	n/a	chr7:21985238-21985252 chr7:21985091-21985100 chr7:21985789-21985800 chr7:21985785-21985793 chr7:21985241-21985255 chr7:21985675-21985685 chr7:21985375-21985384
18	REST	chr7:21984889-21986089	HL-60	blood:	n/a	chr7:21985806-21985819
19	POLR2A	chr7:21984908-21986252	H1-hESC	embryonic stem cell:	n/a	n/a
20	PAX5	chr7:21985002-21985711	GM12878	blood:	n/a	chr7:21985607-21985626
21	MAFK	chr7:21984947-21986261	Hela-S3	cervix:	n/a	n/a
22	EP300	chr7:21985176-21986221	H1-hESC	embryonic stem cell:	n/a	chr7:21985504-21985520 chr7:21985227-21985243 chr7:21985545-21985554 chr7:21985374-21985390 chr7:21985545-21985561 chr7:21985739-21985755
23	POLR2A	chr7:21984951-21986077	PANC-1	pancreas:	n/a	n/a
24	CHD2	chr7:21984318-21986229	H1-hESC	embryonic stem cell:	n/a	chr7:21985502-21985512
25	POLR2A	chr7:21984964-21986082	GM12892	blood:	n/a	n/a
26	POLR2A	chr7:21984829-21985770	HUVEC	blood vessel:	n/a	n/a
27	MYC	chr7:21984247-21986220	NB4	blood:	n/a	chr7:21984693-21984701
28	EP300	chr7:21985266-21986213	GM12878	blood:	n/a	chr7:21985504-21985520 chr7:21985545-21985554 chr7:21985374-21985390 chr7:21985545-21985561 chr7:21985739-21985755
29	ELF1	chr7:21984938-21985935	GM12878	blood:	n/a	n/a
30	ELK1	chr7:21985160-21985798	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:21984829-21986207	U87	brain:	n/a	n/a
32	MAX	chr7:21985122-21986087	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr7:21985291-21985493	HepG2	liver:	n/a	n/a
34	POLR2A	chr7:21984156-21986103	HL-60	blood:	n/a	n/a
35	NR2F2	chr7:21985087-21986321	MCF-7	breast:	n/a	n/a
36	MAX	chr7:21984266-21986319	Hela-S3	cervix:	n/a	chr7:21984693-21984701
37	EGR1	chr7:21985346-21985999	H1-hESC	embryonic stem cell:	n/a	chr7:21985800-21985813
38	MYC	chr7:21985381-21985568	HUVEC	blood vessel:	n/a	n/a
39	RAD21	chr7:21984875-21985584	IMR90	lung:	n/a	chr7:21985128-21985141
40	JUND	chr7:21985331-21985962	A549	lung:	n/a	chr7:21985475-21985483 chr7:21985378-21985387
41	E2F6	chr7:21985150-21986066	K562	blood:	n/a	chr7:21985238-21985252 chr7:21985789-21985800 chr7:21985785-21985793 chr7:21985241-21985255 chr7:21985675-21985685 chr7:21985375-21985384
42	TAF7	chr7:21984918-21986237	H1-hESC	embryonic stem cell:	n/a	n/a
43	SMARCC1	chr7:21984810-21986306	Hela-S3	cervix:	n/a	n/a
44	MYC	chr7:21984346-21986193	MCF10A-Er-Src	breast:	n/a	chr7:21984693-21984701
45	SP1	chr7:21985237-21986204	A549	lung:	n/a	chr7:21985970-21985979 chr7:21986122-21986132
46	EP300	chr7:21985321-21985989	MCF-7	breast:	n/a	chr7:21985504-21985520 chr7:21985545-21985554 chr7:21985374-21985390 chr7:21985545-21985561 chr7:21985739-21985755
47	RCOR1	chr7:21984299-21985874	GM12878	blood:	n/a	n/a
48	MYC	chr7:21984333-21986293	Hela-S3	cervix:	n/a	chr7:21984693-21984701
49	ZNF143	chr7:21985168-21985923	H1-hESC	embryonic stem cell:	n/a	chr7:21985814-21985824
50	POLR2A	chr7:21985236-21985581	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:21985366-21985416	HPAEpiC	pulmonary alveolar:	n/a
2	chr7:21985366-21985416	LNCaP	prostate:	n/a
3	chr7:21985366-21985416	SK-N-SH	brain:	n/a
4	chr7:21985366-21985416	HRE	kidney:	n/a
5	chr7:21985366-21985416	HIPEpiC	eye:	n/a
6	chr7:21985366-21985416	SAEC	small airway:	n/a
7	chr7:21985366-21985416	HRCEpiC	kidney:	n/a
8	chr7:21985366-21985416	SK-N-SH_RA	brain:	n/a
9	chr7:21985366-21985416	HCT-116	colon:	n/a
10	chr7:21985366-21985416	HL-60	blood:	n/a
11	chr7:21985366-21985416	NH-A	brain:	n/a
12	chr7:21985366-21985416	HMEC	breast:	n/a
13	chr7:21985366-21985416	NHDF-neo	bronchial:	n/a
14	chr7:21985366-21985416	MCF10A-Er-Src	breast:	n/a
15	chr7:21985366-21985416	AG09319	gingival:	n/a
16	chr7:21985366-21985416	K562	blood:	n/a
17	chr7:21985366-21985416	HUVEC	blood vessel:	n/a
18	chr7:21985366-21985416	Hela-S3	cervix:	n/a
19	chr7:21985366-21985416	IMR90	lung:	fetal
20	chr7:21985366-21985416	GM12878	blood:	n/a
21	chr7:21985366-21985416	PANC-1	pancreas:	n/a
22	chr7:21985366-21985416	GM19239	blood:	n/a
23	chr7:21985366-21985416	ProgFib	skin:	n/a
24	chr7:21985366-21985416	A549	lung:	n/a
25	chr7:21985366-21985416	BJ	skin:	n/a
26	chr7:21985366-21985416	MCF-7	breast:	n/a
27	chr7:21985366-21985416	Caco-2	colon:	n/a
28	chr7:21985366-21985416	HAEpiC	amniotic membrane:	n/a
29	chr7:21985366-21985416	SK-N-MC	brain:	n/a
30	chr7:21985366-21985416	PrEC	prostate:	n/a
31	chr7:21985366-21985416	HEEpiC	esophagus:	n/a
32	chr7:21985366-21985416	Hepatocyte	liver:	n/a
33	chr7:21985366-21985416	NB4	blood:	n/a
34	chr7:21985366-21985416	U87	brain:	n/a
35	chr7:21985366-21985416	AG04449	skin:	fetal
36	chr7:21985366-21985416	T-47D	breast:	n/a
37	chr7:21985366-21985416	AoSMC	blood vessel:	n/a
38	chr7:21985366-21985416	AG09309	skin:	n/a
39	chr7:21985366-21985416	HepG2	liver:	n/a
40	chr7:21985366-21985416	PFSK-1	brain:	n/a
41	chr7:21985366-21985416	HRPEpiC	eye:	n/a
42	chr7:21985366-21985416	AG04450	lung:	fetal
43	chr7:21985366-21985416	HCF	heart:	n/a
44	chr7:21985366-21985416	GM06990	blood:	n/a
45	chr7:21985366-21985416	NHBE	bronchial:	n/a
46	chr7:21985366-21985416	RPTEC	kidney:	n/a
47	chr7:21985366-21985416	CMK	blood:	n/a
48	chr7:21985366-21985416	HEK293	kidney:	embryo
49	chr7:21985366-21985416	ovcar-3	ovarian:	n/a
50	chr7:21985366-21985416	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:81039964..81040749-chr7:21984789..21985767,2	Hela-S3	cervix:
2	chr19:17580988..17581621-chr7:21984621..21985394,2	Hela-S3	cervix:
3	chr17:73150198..73150857-chr7:21984996..21985582,2	Hela-S3	cervix:
4	chr12:56551838..56552458-chr7:21984929..21985891,2	HCT-116	colon:
5	chr1:152020163..152020789-chr7:21984823..21985554,2	Hela-S3	cervix:
6	chr16:75018623..75019217-chr7:21985015..21985822,2	Hela-S3	cervix:
7	chr3:195269791..195270473-chr7:21985002..21985782,2	Hela-S3	cervix:
8	chr1:86045884..86046584-chr7:21984850..21985841,2	Hela-S3	cervix:
9	chr19:48706732..48707356-chr7:21985245..21986182,2	NB4	blood:
10	chr16:29801700..29802564-chr7:21984791..21985488,2	Hela-S3	cervix:
11	chr7:21984666..21985472-chrX:12993060..12993695,2	Hela-S3	cervix:

Variant related genes	Relation type
CDCA7L	TF binding region
CDCA7L	CpG island
ENSG00000142871	Chromatin interaction
ENSG00000189159	Chromatin interaction
ENSG00000205542	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000130304	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000105483	Chromatin interaction
ENSG00000268583	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000079616	Chromatin interaction
ENSG00000103091	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000184203	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10234020	0.85[AMR][1000 genomes]
rs10246345	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10254656	0.85[AMR][1000 genomes]
rs10254992	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10258599	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10263850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28640950	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6944457	0.84[AFR][1000 genomes];0.85[AMR][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:126 , 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	chr7:21983200-21985800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr7:21983200-21985800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:21983400-21986000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:21983600-21985400	Active TSS	Stomach Smooth Muscle	stomach
6	chr7:21983600-21985800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr7:21983600-21985800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:21983600-21986000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr7:21983600-21986000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr7:21983600-21986000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr7:21983600-21986000	Active TSS	Ovary	ovary
12	chr7:21983600-21986000	Active TSS	Right Ventricle	heart
13	chr7:21983600-21986200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:21983600-21986200	Active TSS	NHDF-Ad	bronchial
15	chr7:21983800-21985400	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr7:21983800-21985400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:21983800-21985400	Active TSS	Fetal Heart	heart
18	chr7:21983800-21985600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:21983800-21985600	Active TSS	Thymus	Thymus
20	chr7:21983800-21985800	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr7:21983800-21985800	Active TSS	GM12878-XiMat	blood
22	chr7:21983800-21985800	Active TSS	NHEK	skin
23	chr7:21983800-21986000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr7:21983800-21986000	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr7:21983800-21986000	Active TSS	Colon Smooth Muscle	Colon
26	chr7:21984000-21985400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr7:21984000-21985400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr7:21984000-21985600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:21984000-21985600	Active TSS	Fetal Intestine Small	intestine
30	chr7:21984000-21985600	Active TSS	Fetal Stomach	stomach
31	chr7:21984000-21985800	Active TSS	H1 Cell Line	embryonic stem cell
32	chr7:21984000-21985800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:21984000-21985800	Active TSS	Fetal Lung	lung
34	chr7:21984000-21985800	Active TSS	HSMMtube	muscle
35	chr7:21984000-21985800	Active TSS	NHLF	lung
36	chr7:21984000-21986000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:21984000-21986000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr7:21984000-21986000	Active TSS	Fetal Kidney	kidney
39	chr7:21984000-21986000	Active TSS	Right Atrium	heart
40	chr7:21984000-21986000	Active TSS	A549	lung
41	chr7:21984000-21986200	Active TSS	H9 Cell Line	embryonic stem cell
42	chr7:21984000-21986200	Active TSS	Brain Angular Gyrus	brain
43	chr7:21984000-21986800	Active TSS	Rectal Smooth Muscle	rectum
44	chr7:21984200-21985600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:21984200-21985600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr7:21984200-21985600	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr7:21984200-21985600	Active TSS	Small Intestine	intestine
48	chr7:21984200-21985800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr7:21984200-21985800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:21984200-21985800	Active TSS	Primary T helper naive cells from peripheral blood	blood

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