Variant report

Variant	rs9840759
Chromosome Location	chr3:157827419-157827420
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	chr3:157827374-157828691	Raji	blood:	n/a	n/a
2	SP1	chr3:157827419-157828075	H1-hESC	embryonic stem cell:	n/a	chr3:157827581-157827595 chr3:157827582-157827591 chr3:157827711-157827722
3	TFAP2C	chr3:157827207-157828603	Hela-S3	cervix:	n/a	chr3:157828138-157828153
4	SP1	chr3:157827378-157828551	A549	lung:	n/a	chr3:157827581-157827595 chr3:157827582-157827591 chr3:157827711-157827722
5	POLR2A	chr3:157827384-157828649	K562	blood:	n/a	n/a
6	FOXM1	chr3:157827383-157828239	GM12878	blood:	n/a	n/a
7	BHLHE40	chr3:157827352-157828810	K562	blood:	n/a	chr3:157828041-157828057
8	HCFC1	chr3:157826392-157829501	Hela-S3	cervix:	n/a	n/a
9	JUND	chr3:157827415-157828474	K562	blood:	n/a	n/a
10	TFAP2A	chr3:157827190-157828568	Hela-S3	cervix:	n/a	chr3:157827375-157827385 chr3:157828237-157828249 chr3:157827373-157827387 chr3:157827375-157827385 chr3:157828030-157828042 chr3:157827373-157827387 chr3:157827373-157827387 chr3:157827375-157827385 chr3:157827375-157827385 chr3:157827373-157827387
11	MAX	chr3:157827379-157828867	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr3:157827160-157830109	K562	blood:	n/a	n/a
13	CHD2	chr3:157827388-157828598	K562	blood:	n/a	chr3:157828301-157828311
14	TRIM28	chr3:157827253-157828222	K562	blood:	n/a	n/a
15	POLR2A	chr3:157827382-157828818	GM12891	blood:	n/a	n/a
16	REST	chr3:157827371-157828648	A549	lung:	n/a	chr3:157827581-157827594
17	PML	chr3:157827407-157828489	K562	blood:	n/a	n/a
18	GTF3C2	chr3:157827232-157827809	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr3:157827369-157828450	H1-neurons	neurons:	n/a	n/a
20	MYC	chr3:157827362-157828985	MCF10A-Er-Src	breast:	n/a	n/a
21	RCOR1	chr3:157827248-157828658	Hela-S3	cervix:	n/a	n/a
22	TEAD4	chr3:157827353-157828022	K562	blood:	n/a	n/a
23	TBP	chr3:157827244-157828769	K562	blood:	n/a	n/a
24	TCF7L2	chr3:157827254-157828496	PANC-1	pancreas:	n/a	n/a
25	MYC	chr3:157827412-157828832	K562	blood:	n/a	n/a
26	POLR2A	chr3:157827311-157828452	SK-N-MC	brain:	n/a	n/a
27	SIN3A	chr3:157827140-157828827	H1-hESC	embryonic stem cell:	n/a	chr3:157827820-157827829
28	KAP1	chr3:157827315-157828787	HEK293	kidney:	n/a	n/a
29	ARID3A	chr3:157827409-157828186	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:157827392-157828589	GM19099	blood:	n/a	n/a
31	RCOR1	chr3:157827369-157828665	K562	blood:	n/a	n/a
32	TCF7L2	chr3:157827306-157828660	Hela-S3	cervix:	n/a	n/a
33	SIN3AK20	chr3:157827257-157828995	MCF-7	breast:	n/a	n/a
34	PML	chr3:157827389-157828302	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:157827301-157828692	K562	blood:	n/a	n/a
36	BCL3	chr3:157827387-157828632	A549	lung:	n/a	chr3:157827920-157827933 chr3:157828036-157828049 chr3:157828134-157828147
37	KAP1	chr3:157827413-157828603	U2OS	brain:	n/a	n/a
38	SRF	chr3:157827276-157828720	MCF-7	breast:	n/a	n/a
39	JUN	chr3:157827150-157828471	K562	blood:	n/a	n/a
40	FOXM1	chr3:157827357-157828361	GM12878	blood:	n/a	n/a
41	BHLHE40	chr3:157827342-157828302	GM12878	blood:	n/a	chr3:157828041-157828057
42	MAFK	chr3:157827123-157828635	K562	blood:	n/a	chr3:157827277-157827288 chr3:157827278-157827289 chr3:157827278-157827289 chr3:157827276-157827290 chr3:157827277-157827288
43	ATF2	chr3:157827405-157828436	GM12878	blood:	n/a	n/a
44	MAX	chr3:157827401-157828829	MCF-7	breast:	n/a	n/a
45	GATA3	chr3:157827339-157828030	T-47D	breast:	n/a	n/a
46	POLR2A	chr3:157827395-157828583	GM18951	blood:	n/a	n/a
47	MAFK	chr3:157827117-157828386	HepG2	liver:	n/a	chr3:157827277-157827288 chr3:157827278-157827289 chr3:157827278-157827289 chr3:157827276-157827290 chr3:157827277-157827288
48	POLR2A	chr3:157827302-157828635	Hela-S3	cervix:	n/a	n/a
49	HCFC1	chr3:157827349-157828704	K562	blood:	n/a	n/a
50	SMC3	chr3:157827342-157828708	Hela-S3	cervix:	n/a	chr3:157828215-157828222 chr3:157828611-157828618

No.	Distal block	Cell Line	Cell type
1	chr3:157821849..157824300-chr3:157826220..157828520,3	MCF-7	breast:
2	chr3:157826605..157829792-chr3:157838040..157843107,6	K562	blood:
3	chr3:157822243..157825572-chr3:157826911..157829349,6	MCF-7	breast:

Variant related genes	Relation type
RSRC1	TF binding region
SHOX2	TF binding region
ENSG00000174891	Chromatin interaction
ENSG00000168779	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10049160	1.00[EUR][1000 genomes]
rs13314233	1.00[EUR][1000 genomes]
rs13323462	1.00[EUR][1000 genomes]
rs13327394	1.00[EUR][1000 genomes]
rs28396261	1.00[EUR][1000 genomes]
rs28646251	1.00[EUR][1000 genomes]
rs28720767	1.00[EUR][1000 genomes]
rs58062483	1.00[EUR][1000 genomes]
rs6762923	1.00[EUR][1000 genomes]
rs6765159	1.00[EUR][1000 genomes]
rs6809280	1.00[EUR][1000 genomes]
rs73021840	1.00[EUR][1000 genomes]
rs73021877	1.00[EUR][1000 genomes]
rs73025925	1.00[EUR][1000 genomes]
rs73025951	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73027918	1.00[EUR][1000 genomes]
rs73028000	1.00[EUR][1000 genomes]
rs73029897	1.00[EUR][1000 genomes]
rs73029899	1.00[EUR][1000 genomes]
rs73031618	1.00[EUR][1000 genomes]
rs73031643	1.00[EUR][1000 genomes]
rs73031646	1.00[EUR][1000 genomes]
rs7613737	1.00[EUR][1000 genomes]
rs9817119	1.00[EUR][1000 genomes]
rs9831137	1.00[EUR][1000 genomes]
rs9838425	1.00[EUR][1000 genomes]
rs9858864	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9869501	1.00[EUR][1000 genomes]
rs9870885	1.00[EUR][1000 genomes]
rs9872495	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9873074	1.00[EUR][1000 genomes]
rs9877843	1.00[EUR][1000 genomes]
rs9877873	1.00[EUR][1000 genomes]
rs9882507	1.00[EUR][1000 genomes]
rs9884071	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	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157826800-157829200	Active TSS	Psoas Muscle	Psoas
2	chr3:157827000-157827600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:157827000-157827600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:157827200-157827600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:157827200-157827600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:157827200-157827600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:157827200-157827600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr3:157827200-157827600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr3:157827200-157827600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr3:157827200-157827600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:157827200-157827600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
12	chr3:157827200-157827600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
13	chr3:157827200-157827600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
14	chr3:157827200-157827600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr3:157827200-157827600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
16	chr3:157827200-157827600	Bivalent/Poised TSS	NH-A	brain
17	chr3:157827200-157827600	Flanking Active TSS	NHEK	skin
18	chr3:157827200-157827800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:157827200-157827800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr3:157827200-157827800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr3:157827200-157827800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr3:157827200-157827800	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr3:157827200-157827800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr3:157827200-157827800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr3:157827200-157827800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr3:157827200-157827800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
27	chr3:157827200-157828000	Active TSS	Primary B cells from cord blood	blood
28	chr3:157827200-157828000	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr3:157827200-157828400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:157827200-157828400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:157827200-157828400	Active TSS	Brain Cingulate Gyrus	brain
32	chr3:157827200-157828400	Active TSS	Right Ventricle	heart
33	chr3:157827200-157828600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:157827200-157828600	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr3:157827200-157828600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:157827200-157828600	Active TSS	Brain Hippocampus Middle	brain
37	chr3:157827200-157828600	Active TSS	Brain Substantia Nigra	brain
38	chr3:157827200-157828600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr3:157827200-157828600	Active TSS	Stomach Smooth Muscle	stomach
40	chr3:157827200-157828600	Bivalent/Poised TSS	HepG2	liver
41	chr3:157827200-157828600	Active TSS	NHDF-Ad	bronchial
42	chr3:157827200-157828800	Active TSS	Right Atrium	heart
43	chr3:157827200-157828800	Active TSS	A549	lung
44	chr3:157827200-157828800	Active TSS	HMEC	breast
45	chr3:157827200-157828800	Active TSS	Osteobl	bone
46	chr3:157827200-157829000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:157827200-157829000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:157827200-157829000	Active TSS	HSMMtube	muscle
49	chr3:157827200-157829600	Active TSS	K562	blood
50	chr3:157827400-157827600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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