Variant report

Variant	rs2271176
Chromosome Location	chr4:122791601-122791602
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	JUND	chr4:122791517-122791699	H1-hESC	embryonic stem cell:	n/a	chr4:122791645-122791654
2	SIN3AK20	chr4:122791399-122791680	HepG2	liver:	n/a	n/a
3	MAX	chr4:122791278-122791906	NB4	blood:	n/a	n/a
4	MAX	chr4:122791133-122791877	ECC-1	luminal epithelium:	n/a	n/a
5	E2F4	chr4:122791326-122791806	MCF10A-Er-Src	breast:	n/a	chr4:122791646-122791655 chr4:122791404-122791414 chr4:122791644-122791653
6	MYC	chr4:122791379-122791679	H1-hESC	embryonic stem cell:	n/a	n/a
7	CREB1	chr4:122791414-122791848	A549	lung:	n/a	chr4:122791643-122791656
8	BRCA1	chr4:122791478-122791826	Hela-S3	cervix:	n/a	n/a
9	TBP	chr4:122790977-122791980	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:122791436-122791717	HepG2	liver:	n/a	n/a
11	POLR2A	chr4:122791350-122791916	GM10847	blood:	n/a	n/a
12	NR2F2	chr4:122791393-122791803	K562	blood:	n/a	n/a
13	RFX5	chr4:122790441-122792314	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr4:122791262-122791891	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr4:122791220-122791748	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:122791420-122791714	PANC-1	pancreas:	n/a	n/a
17	CTCF	chr4:122791560-122791712	Spleen_OC	spleen:	n/a	n/a
18	MAX	chr4:122791513-122791882	HepG2	liver:	n/a	n/a
19	ELK1	chr4:122791245-122791799	Hela-S3	cervix:	n/a	n/a
20	CBX3	chr4:122791371-122791855	K562	blood:	n/a	n/a
21	CREB1	chr4:122791451-122791777	A549	lung:	n/a	chr4:122791643-122791656
22	POLR2A	chr4:122791324-122791908	K562	blood:	n/a	n/a
23	POLR2A	chr4:122791287-122791729	GM12892	blood:	n/a	n/a
24	REST	chr4:122791351-122791754	HepG2	liver:	n/a	n/a
25	ARID3A	chr4:122791429-122791606	HepG2	liver:	n/a	n/a
26	POLR2A	chr4:122791316-122791714	GM12878	blood:	n/a	n/a
27	NFYB	chr4:122791568-122791939	GM12878	blood:	n/a	n/a
28	EBF1	chr4:122791446-122791921	GM12878	blood:	n/a	n/a
29	IRF1	chr4:122791373-122791974	K562	blood:	n/a	chr4:122791687-122791701 chr4:122791706-122791720
30	TEAD4	chr4:122791307-122792042	K562	blood:	n/a	n/a
31	ZMIZ1	chr4:122791355-122791764	K562	blood:	n/a	n/a
32	POLR2A	chr4:122791140-122792018	Raji	blood:	n/a	n/a
33	POLR2A	chr4:122791283-122791821	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr4:122791215-122791938	Gliobla	brain:	n/a	n/a
35	POLR2A	chr4:122791356-122791695	SK-N-SH	brain:	n/a	n/a
36	ZNF263	chr4:122790685-122791782	HEK293-T-REx	kidney:	n/a	chr4:122791128-122791137
37	MAX	chr4:122791235-122792027	A549	lung:	n/a	n/a
38	RAD21	chr4:122791325-122791653	H1-hESC	embryonic stem cell:	n/a	chr4:122791330-122791344
39	GATA1	chr4:122790867-122792641	K562	blood:	n/a	chr4:122791879-122791895
40	TAF1	chr4:122791434-122791655	SK-N-SH	brain:	n/a	n/a
41	SP1	chr4:122791305-122791855	A549	lung:	n/a	chr4:122791695-122791702 chr4:122791689-122791701 chr4:122791832-122791845 chr4:122791689-122791701 chr4:122791690-122791699
42	MAX	chr4:122791235-122791909	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr4:122791290-122791878	GM12878	blood:	n/a	n/a
44	ELF1	chr4:122791455-122791841	K562	blood:	n/a	n/a
45	POLR2A	chr4:122791359-122791738	HepG2	liver:	n/a	n/a
46	POLR2A	chr4:122791261-122791740	GM12892	blood:	n/a	n/a
47	UBTF	chr4:122791345-122791684	K562	blood:	n/a	n/a
48	MXI1	chr4:122791117-122791895	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr4:122791252-122791823	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:122791195-122791827	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:122743665..122745647-chr4:122789959..122792844,2	K562	blood:
2	chr4:122743937..122745709-chr4:122789073..122792833,3	MCF-7	breast:
3	chr1:227505645..227506241-chr4:122791074..122791739,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000261501	TF binding region
ENSG00000145386	Chromatin interaction
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10001889	0.92[ASN][1000 genomes]
rs10004284	0.92[ASN][1000 genomes]
rs10007956	0.92[ASN][1000 genomes]
rs10013916	0.92[ASN][1000 genomes]
rs10023020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10024820	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10084948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048433	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098643	0.92[ASN][1000 genomes]
rs11724322	0.91[ASN][1000 genomes]
rs11732666	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs11733882	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11734075	0.89[ASN][1000 genomes]
rs12510839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13106764	0.92[ASN][1000 genomes]
rs13108360	0.82[ASN][1000 genomes]
rs13119055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13119958	0.80[ASN][1000 genomes]
rs13121963	0.82[ASN][1000 genomes]
rs13127488	0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs13130789	0.85[ASN][1000 genomes]
rs13131003	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs13133876	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13138774	0.81[ASN][1000 genomes]
rs13140070	0.92[ASN][1000 genomes]
rs13143218	0.96[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs13145213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13151345	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs13152701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1507993	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs17005256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292232	0.82[CHB][hapmap]
rs28435300	0.92[ASN][1000 genomes]
rs28522256	0.92[ASN][1000 genomes]
rs28672860	0.92[ASN][1000 genomes]
rs3217772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34445121	0.92[ASN][1000 genomes]
rs35341163	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35495505	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805158	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3805161	0.82[CHB][hapmap]
rs3811742	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]
rs41462746	0.88[YRI][hapmap]
rs4256243	0.88[YRI][hapmap]
rs4833233	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4833234	0.89[ASN][1000 genomes]
rs4833235	0.89[ASN][1000 genomes]
rs4833236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833773	0.85[ASN][1000 genomes]
rs4833775	0.92[ASN][1000 genomes]
rs4833777	0.81[ASN][1000 genomes]
rs4833778	0.82[CHB][hapmap]
rs5004355	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67150579	0.92[ASN][1000 genomes]
rs67775544	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6811867	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6830443	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845901	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs769236	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs884701	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs951974	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs953691	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs966555	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9995319	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9998785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9999362	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2271176	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs2271176	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL
rs2271176	CCNA2	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122790000-122792000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr4:122790000-122792200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr4:122790000-122792200	Active TSS	Brain Angular Gyrus	brain
4	chr4:122790200-122792000	Active TSS	Brain Cingulate Gyrus	brain
5	chr4:122790200-122792200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:122790200-122792200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr4:122790200-122792200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:122790200-122792200	Active TSS	Fetal Brain Female	brain
9	chr4:122790400-122791800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:122790400-122792000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr4:122790400-122792000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr4:122790400-122792000	Active TSS	Rectal Smooth Muscle	rectum
13	chr4:122790400-122792000	Active TSS	GM12878-XiMat	blood
14	chr4:122790400-122792200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:122790400-122792200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr4:122790400-122792200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:122790400-122792200	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:122790400-122792200	Active TSS	A549	lung
19	chr4:122790400-122792200	Active TSS	HMEC	breast
20	chr4:122790400-122792400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:122790600-122791800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:122790600-122792000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr4:122790600-122792000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr4:122790600-122792000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:122790600-122792000	Active TSS	Muscle Satellite Cultured Cells	--
26	chr4:122790600-122792000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:122790600-122792000	Active TSS	Left Ventricle	heart
28	chr4:122790600-122792000	Active TSS	HSMM	muscle
29	chr4:122790600-122792200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr4:122790600-122792200	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr4:122790600-122792200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr4:122790600-122792200	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr4:122790600-122792200	Active TSS	Primary T cells from cord blood	blood
34	chr4:122790600-122792200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr4:122790600-122792200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:122790600-122792200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:122790600-122792200	Active TSS	Fetal Intestine Small	intestine
38	chr4:122790600-122792200	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr4:122790600-122792200	Active TSS	Right Atrium	heart
40	chr4:122790600-122792200	Active TSS	HSMMtube	muscle
41	chr4:122790600-122792200	Active TSS	NHDF-Ad	bronchial
42	chr4:122790600-122792400	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr4:122790600-122792400	Active TSS	Right Ventricle	heart
44	chr4:122790600-122792400	Active TSS	Hela-S3	cervix
45	chr4:122790800-122791800	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr4:122790800-122791800	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr4:122790800-122791800	Active TSS	HUVEC	blood vessel
48	chr4:122790800-122791800	Active TSS	NHEK	skin
49	chr4:122790800-122791800	Active TSS	Osteobl	bone
50	chr4:122790800-122792000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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