Variant report

Variant	rs41274648
Chromosome Location	chr9:101984378-101984379
allele	C/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	chr9:101983503-101985162	GM18526	blood:	n/a	n/a
2	GATA3	chr9:101984086-101984447	T-47D	breast:	n/a	n/a
3	MYC	chr9:101983427-101985008	A549	lung:	n/a	chr9:101984740-101984750
4	HEY1	chr9:101984363-101984859	HepG2	liver:	n/a	n/a
5	MAFF	chr9:101984246-101984523	K562	blood:	n/a	n/a
6	ATF1	chr9:101984110-101984717	K562	blood:	n/a	n/a
7	MAZ	chr9:101983070-101985271	IMR90	lung:	n/a	chr9:101984740-101984750
8	TCF12	chr9:101983632-101984647	ECC-1	luminal epithelium:	n/a	chr9:101984570-101984577 chr9:101984248-101984255 chr9:101984247-101984257
9	SP1	chr9:101983987-101984772	H1-hESC	embryonic stem cell:	n/a	chr9:101984545-101984557 chr9:101984267-101984279 chr9:101984669-101984678 chr9:101984546-101984555 chr9:101984268-101984277 chr9:101984546-101984556 chr9:101984547-101984556 chr9:101984546-101984556 chr9:101984545-101984557 chr9:101984547-101984556 chr9:101984267-101984279
10	NR2C2	chr9:101984096-101984679	HepG2	liver:	n/a	n/a
11	ZNF143	chr9:101983864-101984809	Hela-S3	cervix:	n/a	chr9:101984671-101984689
12	EGR1	chr9:101984001-101984847	GM12878	blood:	n/a	chr9:101984546-101984556 chr9:101984541-101984554 chr9:101984537-101984559 chr9:101984269-101984279
13	SMC3	chr9:101984094-101984499	K562	blood:	n/a	n/a
14	MAX	chr9:101983712-101984961	A549	lung:	n/a	chr9:101984740-101984750
15	EBF1	chr9:101984306-101984681	GM12878	blood:	n/a	chr9:101984511-101984520
16	BCLAF1	chr9:101983659-101985001	GM12878	blood:	n/a	chr9:101983808-101983821 chr9:101983770-101983783 chr9:101983767-101983780
17	MAX	chr9:101983531-101985067	A549	lung:	n/a	chr9:101984740-101984750
18	EGR1	chr9:101983882-101984888	K562	blood:	n/a	chr9:101984546-101984556 chr9:101984541-101984554 chr9:101984537-101984559 chr9:101984269-101984279
19	EBF1	chr9:101984047-101984666	GM12878	blood:	n/a	chr9:101984511-101984520
20	BRCA1	chr9:101983978-101984608	GM12878	blood:	n/a	n/a
21	TBP	chr9:101983367-101985181	HepG2	liver:	n/a	n/a
22	FOS	chr9:101984290-101984725	MCF10A-Er-Src	breast:	n/a	n/a
23	MXI1	chr9:101983762-101984670	K562	blood:	n/a	n/a
24	POLR2A	chr9:101983870-101984792	U87	brain:	n/a	n/a
25	MAX	chr9:101983352-101985231	MCF-7	breast:	n/a	chr9:101984740-101984750
26	CEBPB	chr9:101984019-101984678	Hela-S3	cervix:	n/a	n/a
27	MAFK	chr9:101984119-101984989	HepG2	liver:	n/a	n/a
28	TAF1	chr9:101983639-101984832	MCF-7	breast:	n/a	n/a
29	ZKSCAN1	chr9:101983811-101984540	Hela-S3	cervix:	n/a	n/a
30	MAX	chr9:101983554-101985222	HepG2	liver:	n/a	chr9:101984740-101984750
31	SP4	chr9:101983920-101984793	H1-hESC	embryonic stem cell:	n/a	chr9:101984541-101984557 chr9:101984543-101984559
32	TAF1	chr9:101983864-101984788	GM12892	blood:	n/a	n/a
33	STAT5A	chr9:101983952-101984588	GM12878	blood:	n/a	n/a
34	POLR2A	chr9:101983199-101985664	GM12891	blood:	n/a	n/a
35	POLR2A	chr9:101983605-101985074	HL-60	blood:	n/a	n/a
36	NFIC	chr9:101983804-101984732	HepG2	liver:	n/a	n/a
37	EP300	chr9:101984044-101984696	GM12878	blood:	n/a	n/a
38	KAP1	chr9:101984018-101984650	U2OS	brain:	n/a	n/a
39	YY1	chr9:101983761-101985358	GM12878	blood:	n/a	chr9:101984546-101984555 chr9:101983812-101983823 chr9:101984782-101984793 chr9:101983812-101983821 chr9:101983807-101983821 chr9:101984778-101984789
40	SP1	chr9:101983811-101984956	A549	lung:	n/a	chr9:101984545-101984557 chr9:101984267-101984279 chr9:101984669-101984678 chr9:101984546-101984555 chr9:101984268-101984277 chr9:101984546-101984556 chr9:101984547-101984556 chr9:101984546-101984556 chr9:101984545-101984557 chr9:101984547-101984556 chr9:101984267-101984279
41	JUND	chr9:101984033-101984474	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr9:101983798-101984828	HCT-116	colon:	n/a	n/a
43	SMARCB1	chr9:101983425-101984984	Hela-S3	cervix:	n/a	n/a
44	MAX	chr9:101983279-101985191	K562	blood:	n/a	chr9:101984740-101984750
45	SIN3AK20	chr9:101983486-101985000	K562	blood:	n/a	n/a
46	MAX	chr9:101983788-101984913	HUVEC	blood vessel:	n/a	chr9:101984740-101984750
47	MAX	chr9:101983263-101984769	Hela-S3	cervix:	n/a	chr9:101984740-101984750
48	SIX5	chr9:101984055-101984663	A549	lung:	n/a	n/a
49	MAX	chr9:101983747-101985039	HepG2	liver:	n/a	chr9:101984740-101984750
50	TCF3	chr9:101983957-101984721	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45285339..45286064-chr9:101983836..101984535,2	HCT-116	colon:
2	chr1:182359515..182361147-chr9:101982675..101984473,2	K562	blood:
3	chr9:101982726..101986093-chr9:102580219..102583469,4	K562	blood:
4	chr9:101983887..101986630-chr9:131936174..131938909,2	MCF-7	breast:
5	chr9:101945788..101948395-chr9:101983472..101985266,3	MCF-7	breast:
6	chr6:27100663..27101358-chr9:101983914..101984541,2	Hela-S3	cervix:
7	chr9:101983020..101985403-chr9:102581774..102586122,4	MCF-7	breast:
8	chr17:75315317..75315846-chr9:101984007..101984890,2	HCT-116	colon:
9	chr9:101982802..101985328-chr9:102065308..102068359,3	MCF-7	breast:
10	chr4:91048485..91049157-chr9:101983883..101984451,2	Hela-S3	cervix:

Variant related genes	Relation type
ALG2	TF binding region
SEC61B	TF binding region
ENSG00000237461	Chromatin interaction
ENSG00000255815	Chromatin interaction
ENSG00000119508	Chromatin interaction
ENSG00000184640	Chromatin interaction
ENSG00000135821	Chromatin interaction
ENSG00000240235	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000268050	Chromatin interaction
ENSG00000184305	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10819642	0.87[EUR][1000 genomes]
rs11545137	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788822	0.89[AMR][1000 genomes]
rs12002203	0.87[ASN][1000 genomes]
rs12003123	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12005715	0.87[ASN][1000 genomes]
rs16918376	0.87[ASN][1000 genomes]
rs17725470	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17725597	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17725608	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17725644	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17725679	0.87[ASN][1000 genomes]
rs17725720	0.87[ASN][1000 genomes]
rs17787503	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17787533	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17787606	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28608552	0.87[ASN][1000 genomes]
rs35626507	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780616	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41274646	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265241	0.87[ASN][1000 genomes]
rs4554535	0.87[ASN][1000 genomes]
rs55676416	0.87[ASN][1000 genomes]
rs58644416	0.87[ASN][1000 genomes]
rs73653775	0.87[ASN][1000 genomes]
rs7857426	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7863354	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101981600-101985600	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr9:101981600-101985800	Active TSS	GM12878-XiMat	blood
3	chr9:101982000-101985600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:101982000-101986000	Active TSS	Right Atrium	heart
5	chr9:101982000-101986200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:101982200-101985400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr9:101982200-101985400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr9:101982200-101985800	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr9:101982200-101985800	Active TSS	Psoas Muscle	Psoas
10	chr9:101982400-101985400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr9:101982400-101985600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr9:101982400-101986000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:101982400-101986000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr9:101982400-101986000	Active TSS	Right Ventricle	heart
15	chr9:101982600-101985000	Active TSS	Duodenum Mucosa	Duodenum
16	chr9:101982600-101985200	Active TSS	Hela-S3	cervix
17	chr9:101982600-101985400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:101982600-101985600	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr9:101982600-101985800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:101982600-101986000	Active TSS	HSMM	muscle
21	chr9:101982600-101986200	Active TSS	Pancreas	Pancrea
22	chr9:101982800-101985200	Active TSS	K562	blood
23	chr9:101982800-101985400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:101982800-101985400	Active TSS	HMEC	breast
25	chr9:101982800-101985600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:101983000-101985200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr9:101983000-101985200	Active TSS	Fetal Kidney	kidney
28	chr9:101983000-101985400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr9:101983000-101985400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr9:101983000-101985400	Active TSS	Fetal Intestine Large	intestine
31	chr9:101983000-101985600	Active TSS	Ovary	ovary
32	chr9:101983000-101985800	Active TSS	NHDF-Ad	bronchial
33	chr9:101983000-101986000	Active TSS	A549	lung
34	chr9:101983200-101985000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:101983200-101985000	Active TSS	Colonic Mucosa	Colon
36	chr9:101983200-101985200	Active TSS	Brain Substantia Nigra	brain
37	chr9:101983200-101985400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:101983200-101985400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:101983200-101985400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:101983200-101985400	Active TSS	Esophagus	oesophagus
41	chr9:101983200-101985400	Active TSS	Placenta Amnion	Placenta Amnion
42	chr9:101983200-101985400	Active TSS	Stomach Mucosa	stomach
43	chr9:101983200-101985400	Active TSS	NH-A	brain
44	chr9:101983200-101985600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr9:101983200-101985600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:101983200-101985600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:101983200-101985600	Active TSS	Gastric	stomach
48	chr9:101983200-101985600	Active TSS	Left Ventricle	heart
49	chr9:101983200-101985600	Bivalent/Poised TSS	HepG2	liver
50	chr9:101983200-101985800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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