Variant report

Variant	rs1441742
Chromosome Location	chr10:90639810-90639811
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	E2F4	chr10:90639687-90639887	MCF10A-Er-Src	breast:	n/a	n/a
2	TAF1	chr10:90639558-90641029	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr10:90639586-90641828	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr10:90639480-90641613	U87	brain:	n/a	n/a
5	POLR2A	chr10:90639409-90641040	GM12892	blood:	n/a	n/a
6	MAX	chr10:90639494-90640977	A549	lung:	n/a	chr10:90640816-90640826
7	POLR2A	chr10:90639614-90640945	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:90639531-90641494	GM18951	blood:	n/a	n/a
9	BHLHE40	chr10:90639378-90640927	GM12878	blood:	n/a	chr10:90640674-90640690
10	MXI1	chr10:90639555-90641039	GM12878	blood:	n/a	n/a
11	RELA	chr10:90639656-90640919	GM19193	blood:	n/a	n/a
12	POLR2A	chr10:90639757-90640952	MCF-7	breast:	n/a	n/a
13	STAT1	chr10:90639768-90640950	GM12878	blood:	n/a	chr10:90640658-90640666
14	MXI1	chr10:90639810-90640803	HepG2	liver:	n/a	n/a
15	WRNIP1	chr10:90639531-90640975	GM12878	blood:	n/a	n/a
16	TAF1	chr10:90639624-90640943	GM12878	blood:	n/a	n/a
17	RAD21	chr10:90639665-90640999	ECC-1	luminal epithelium:	n/a	chr10:90640670-90640684
18	POLR2A	chr10:90639563-90641024	GM12891	blood:	n/a	n/a
19	YY1	chr10:90639765-90640791	GM12891	blood:	n/a	chr10:90639922-90639931 chr10:90639917-90639931 chr10:90639919-90639928 chr10:90640598-90640607 chr10:90639919-90639930
20	TCF3	chr10:90639660-90640760	GM12878	blood:	n/a	n/a
21	TCF12	chr10:90639595-90641139	A549	lung:	n/a	n/a
22	MAX	chr10:90639806-90640952	HepG2	liver:	n/a	chr10:90640816-90640826
23	TAF1	chr10:90639721-90640483	GM12891	blood:	n/a	n/a
24	MTA3	chr10:90639449-90640307	GM12878	blood:	n/a	n/a
25	MAX	chr10:90639660-90640949	MCF-7	breast:	n/a	chr10:90640816-90640826
26	POLR2A	chr10:90639293-90641628	GM12892	blood:	n/a	n/a
27	ZKSCAN1	chr10:90639600-90640908	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr10:90639521-90641000	HL-60	blood:	n/a	n/a
29	TEAD4	chr10:90639599-90640824	ECC-1	luminal epithelium:	n/a	n/a
30	KAP1	chr10:90639269-90640641	HEK293	kidney:	n/a	n/a
31	ZEB1	chr10:90639774-90640951	GM12878	blood:	n/a	chr10:90640925-90640937 chr10:90640927-90640934
32	TAF1	chr10:90639622-90639893	GM12892	blood:	n/a	n/a
33	HA-E2F1	chr10:90639758-90640843	Hela-S3	cervix:	n/a	chr10:90639917-90639927 chr10:90639920-90639930 chr10:90640546-90640553
34	POLR2A	chr10:90639591-90641016	GM12891	blood:	n/a	n/a
35	YY1	chr10:90639582-90640925	ECC-1	luminal epithelium:	n/a	chr10:90639922-90639931 chr10:90639917-90639931 chr10:90639919-90639928 chr10:90640598-90640607 chr10:90639919-90639930
36	BCLAF1	chr10:90639559-90641144	GM12878	blood:	n/a	chr10:90639918-90639927 chr10:90639921-90639930 chr10:90639918-90639931
37	REST	chr10:90639720-90640575	SK-N-SH	brain:	n/a	n/a
38	TAF1	chr10:90639721-90640041	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr10:90639363-90641045	HL-60	blood:	n/a	n/a
40	POLR2A	chr10:90639648-90640949	GM12878	blood:	n/a	n/a
41	RFX5	chr10:90639434-90640877	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr10:90639722-90640870	HCT-116	colon:	n/a	n/a
43	MYC	chr10:90639496-90639828	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr10:90639733-90640809	HCT-116	colon:	n/a	n/a
45	POLR2A	chr10:90639519-90641333	GM15510	blood:	n/a	n/a
46	POLR2A	chr10:90639558-90641614	U87	brain:	n/a	n/a
47	RELA	chr10:90639550-90641028	GM19099	blood:	n/a	n/a
48	TAF1	chr10:90639625-90640880	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr10:90639689-90641264	MCF10A-Er-Src	breast:	n/a	n/a
50	MYC	chr10:90639569-90641297	Hela-S3	cervix:	n/a	chr10:90640816-90640826

No.	Distal block	Cell Line	Cell type
1	chr10:90639734..90640291-chr9:86595257..86596036,2	Hela-S3	cervix:
2	chr10:90639301..90642051-chr10:90749823..90751899,2	MCF-7	breast:
3	chr1:46151781..46152462-chr10:90639721..90640246,2	Hela-S3	cervix:
4	chr10:90634887..90637855-chr10:90638729..90640945,2	MCF-7	breast:
5	chr1:150550552..150551301-chr10:90639551..90640288,2	Hela-S3	cervix:

Variant related genes	Relation type
STAMBPL1	TF binding region
ENSG00000234256	Chromatin interaction
ENSG00000107796	Chromatin interaction
ENSG00000178966	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000026103	Chromatin interaction
ENSG00000165119	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11202878	0.81[ASN][1000 genomes]
rs12248501	0.81[ASN][1000 genomes]
rs17113812	0.85[AFR][1000 genomes]
rs74147302	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs74150104	0.87[AFR][1000 genomes]
rs7911566	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr10:90639000-90642200	Active TSS	Rectal Smooth Muscle	rectum
2	chr10:90639200-90640000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:90639200-90640000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:90639200-90640000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
5	chr10:90639200-90640200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:90639200-90640800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr10:90639200-90641200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr10:90639200-90642000	Active TSS	Brain Cingulate Gyrus	brain
9	chr10:90639200-90642000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr10:90639200-90642400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:90639400-90640000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:90639400-90640000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr10:90639400-90640000	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr10:90639400-90640000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr10:90639400-90640000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr10:90639400-90640000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:90639400-90640000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:90639400-90640000	Flanking Active TSS	Fetal Brain Male	brain
19	chr10:90639400-90640000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr10:90639400-90640200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr10:90639400-90640200	Flanking Active TSS	HMEC	breast
22	chr10:90639400-90640400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
23	chr10:90639400-90641000	Active TSS	NH-A	brain
24	chr10:90639400-90641200	Active TSS	H1 Cell Line	embryonic stem cell
25	chr10:90639400-90641200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr10:90639400-90641200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr10:90639400-90641200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr10:90639400-90641200	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr10:90639400-90641200	Active TSS	HSMM	muscle
30	chr10:90639400-90641400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr10:90639400-90641400	Active TSS	Brain Angular Gyrus	brain
32	chr10:90639400-90641400	Active TSS	Brain Substantia Nigra	brain
33	chr10:90639400-90641400	Active TSS	HSMMtube	muscle
34	chr10:90639400-90641800	Active TSS	Ovary	ovary
35	chr10:90639400-90642000	Active TSS	Right Atrium	heart
36	chr10:90639400-90642400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr10:90639600-90640000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr10:90639600-90640000	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr10:90639600-90640000	Flanking Active TSS	Fetal Thymus	thymus
40	chr10:90639600-90640000	Active TSS	Psoas Muscle	Psoas
41	chr10:90639600-90640000	Flanking Active TSS	HUVEC	blood vessel
42	chr10:90639600-90640200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr10:90639600-90640200	Flanking Active TSS	Placenta	Placenta
44	chr10:90639600-90640200	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr10:90639600-90640400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
46	chr10:90639600-90640600	Active TSS	Brain Hippocampus Middle	brain
47	chr10:90639600-90640800	Active TSS	Aorta	Aorta
48	chr10:90639600-90640800	Active TSS	Stomach Mucosa	stomach
49	chr10:90639600-90640800	Active TSS	K562	blood
50	chr10:90639600-90641000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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