Variant report

Variant	rs3811742
Chromosome Location	chr4:122722693-122722694
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:350)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:350 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr4:122722284-122722726	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:122721839-122722804	HUVEC	blood vessel:	n/a	n/a
3	NRF1	chr4:122722211-122722703	H1-hESC	embryonic stem cell:	n/a	chr4:122722414-122722425
4	SPI1	chr4:122721986-122722699	GM12878	blood:	n/a	chr4:122722188-122722201
5	POLR2A	chr4:122721912-122722840	Hela-S3	cervix:	n/a	n/a
6	GABPA	chr4:122722253-122722748	MCF-7	breast:	n/a	n/a
7	RCOR1	chr4:122721583-122723102	K562	blood:	n/a	n/a
8	EP300	chr4:122721679-122722781	K562	blood:	n/a	n/a
9	MAZ	chr4:122722285-122722867	Hela-S3	cervix:	n/a	n/a
10	ATF1	chr4:122721993-122722724	K562	blood:	n/a	n/a
11	MAX	chr4:122722272-122722827	K562	blood:	n/a	n/a
12	CREB1	chr4:122722179-122722774	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr4:122721941-122722815	SK-N-SH	brain:	n/a	n/a
14	ZMIZ1	chr4:122722009-122723027	K562	blood:	n/a	n/a
15	SIN3AK20	chr4:122722027-122722840	SK-N-SH	brain:	n/a	n/a
16	CUX1	chr4:122721558-122722805	GM12878	blood:	n/a	chr4:122722260-122722274
17	POLR2A	chr4:122721994-122722696	GM10847	blood:	n/a	n/a
18	JUN	chr4:122720661-122723088	K562	blood:	n/a	chr4:122722469-122722482
19	PML	chr4:122721797-122722876	K562	blood:	n/a	chr4:122721878-122721886
20	STAT5A	chr4:122721693-122722936	GM12878	blood:	n/a	n/a
21	MAX	chr4:122722044-122722694	A549	lung:	n/a	n/a
22	SMC3	chr4:122722185-122722871	Hela-S3	cervix:	n/a	n/a
23	SRF	chr4:122722186-122722783	ECC-1	luminal epithelium:	n/a	n/a
24	IRF4	chr4:122721926-122722813	GM12878	blood:	n/a	n/a
25	POLR2A	chr4:122721923-122722772	GM12878	blood:	n/a	n/a
26	YY1	chr4:122722014-122722713	SK-N-SH	brain:	n/a	chr4:122722458-122722467
27	HEY1	chr4:122721835-122722736	K562	blood:	n/a	n/a
28	ELF1	chr4:122722151-122722850	MCF-7	breast:	n/a	chr4:122722721-122722733 chr4:122722458-122722467
29	POLR2A	chr4:122722149-122722759	HepG2	liver:	n/a	n/a
30	POLR2A	chr4:122722059-122722723	PANC-1	pancreas:	n/a	n/a
31	MAX	chr4:122722111-122722923	A549	lung:	n/a	n/a
32	POLR2A	chr4:122721793-122723191	Hela-S3	cervix:	n/a	n/a
33	SRF	chr4:122722013-122723016	HCT-116	colon:	n/a	n/a
34	POLR2A	chr4:122721735-122723063	K562	blood:	n/a	n/a
35	POLR2A	chr4:122721915-122722804	GM12891	blood:	n/a	n/a
36	YY1	chr4:122721986-122722698	GM12891	blood:	n/a	chr4:122722458-122722467
37	MYC	chr4:122722136-122722874	NB4	blood:	n/a	n/a
38	ELF1	chr4:122722247-122722700	K562	blood:	n/a	chr4:122722458-122722467
39	POLR2A	chr4:122722133-122722838	MCF-7	breast:	n/a	n/a
40	TAF1	chr4:122721953-122722911	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr4:122721822-122722846	GM18951	blood:	n/a	n/a
42	POLR2A	chr4:122721440-122722876	GM12878	blood:	n/a	n/a
43	RCOR1	chr4:122722207-122722920	HepG2	liver:	n/a	n/a
44	CHD2	chr4:122722374-122722768	HepG2	liver:	n/a	n/a
45	POLR2A	chr4:122721713-122722868	GM12892	blood:	n/a	n/a
46	MXI1	chr4:122721554-122722712	K562	blood:	n/a	n/a
47	SPI1	chr4:122721984-122722832	HL-60	blood:	n/a	chr4:122722188-122722201
48	TBL1XR1	chr4:122721657-122722771	K562	blood:	n/a	n/a
49	REST	chr4:122722021-122722763	K562	blood:	n/a	n/a
50	SRF	chr4:122722228-122722700	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:122721925..122722763-chr5:57755619..57756423,2	HCT-116	colon:
2	chr4:122721460..122723006-chr4:122781876..122783568,2	K562	blood:
3	chr4:122722106..122722889-chr6:43020654..43021622,2	Hela-S3	cervix:
4	chr4:122719927..122724442-chr4:122741540..122746604,11	MCF-7	breast:
5	chr4:122720772..122725008-chr4:122725244..122729002,8	K562	blood:
6	chr4:122616868..122619074-chr4:122720747..122723892,4	MCF-7	breast:

No data

Variant related genes	Relation type
EXOSC9	TF binding region
ENSG00000044090	Chromatin interaction
ENSG00000123737	Chromatin interaction
ENSG00000164111	Chromatin interaction
ENSG00000145632	Chromatin interaction
ENSG00000145386	Chromatin interaction
ENSG00000138686	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10001889	0.97[ASN][1000 genomes]
rs10004284	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10007956	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10013916	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10023020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10024820	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10084948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1048433	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098643	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11724322	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11732666	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs11733882	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11734075	0.94[ASN][1000 genomes]
rs12510839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13106764	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13108419	0.81[ASN][1000 genomes]
rs13119055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127488	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs13130789	0.90[ASN][1000 genomes]
rs13131003	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13133876	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13140070	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13143218	0.96[CHB][hapmap];0.87[JPT][hapmap]
rs13145213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13151345	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13152701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1507993	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17005256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292232	0.82[CHB][hapmap]
rs28435300	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28522256	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28672860	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3217772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34445121	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35341163	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35495505	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3762840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805158	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3805161	0.82[CHB][hapmap]
rs41462746	0.88[YRI][hapmap]
rs4256243	0.88[YRI][hapmap]
rs4833233	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4833234	0.94[ASN][1000 genomes]
rs4833235	0.94[ASN][1000 genomes]
rs4833236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4833773	0.90[ASN][1000 genomes]
rs4833775	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4833778	0.82[CHB][hapmap]
rs5004355	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67150579	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67775544	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6811867	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6830443	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845901	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs769236	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884701	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs951974	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs953691	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs966555	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9995319	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9998785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999362	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3811742	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs3811742	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122721200-122722800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:122721200-122723600	Active TSS	Thymus	Thymus
3	chr4:122721400-122723200	Active TSS	K562	blood
4	chr4:122721600-122722800	Active TSS	Stomach Smooth Muscle	stomach
5	chr4:122721600-122723000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:122721600-122723000	Active TSS	Brain Anterior Caudate	brain
7	chr4:122721600-122723000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr4:122721600-122723200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr4:122721600-122723200	Active TSS	Primary T cells fromperipheralblood	blood
10	chr4:122721600-122723200	Active TSS	Brain Angular Gyrus	brain
11	chr4:122721600-122723400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:122721600-122723600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:122721800-122722800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr4:122721800-122723000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:122721800-122723000	Active TSS	Aorta	Aorta
16	chr4:122721800-122723000	Active TSS	Brain Substantia Nigra	brain
17	chr4:122721800-122723000	Active TSS	Left Ventricle	heart
18	chr4:122721800-122723200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr4:122721800-122723200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:122721800-122723200	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr4:122721800-122723200	Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr4:122721800-122723200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:122721800-122723200	Active TSS	Colonic Mucosa	Colon
24	chr4:122721800-122723200	Active TSS	Fetal Kidney	kidney
25	chr4:122721800-122723200	Active TSS	Fetal Muscle Trunk	muscle
26	chr4:122721800-122723200	Active TSS	Placenta	Placenta
27	chr4:122721800-122723200	Active TSS	Ovary	ovary
28	chr4:122721800-122723200	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr4:122721800-122723200	Active TSS	Right Ventricle	heart
30	chr4:122721800-122723200	Active TSS	HSMMtube	muscle
31	chr4:122721800-122723200	Active TSS	NHLF	lung
32	chr4:122721800-122723400	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr4:122721800-122723400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:122721800-122723400	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr4:122721800-122723400	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr4:122721800-122723400	Active TSS	Brain Germinal Matrix	brain
37	chr4:122721800-122723400	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr4:122721800-122723400	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr4:122721800-122723400	Active TSS	Right Atrium	heart
40	chr4:122721800-122723600	Active TSS	H1 Cell Line	embryonic stem cell
41	chr4:122721800-122723600	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr4:122721800-122723600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:122721800-122723600	Active TSS	Psoas Muscle	Psoas
44	chr4:122721800-122723800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:122722000-122722800	Active TSS	Primary B cells from peripheral blood	blood
46	chr4:122722000-122722800	Active TSS	Primary T cells from cord blood	blood
47	chr4:122722000-122722800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:122722000-122722800	Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr4:122722000-122723000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:122722000-122723000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--

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