Variant report

Variant	rs213887
Chromosome Location	chr5:94982711-94982712
allele	A/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	USF2	chr5:94982146-94983239	Hela-S3	cervix:	n/a	chr5:94982415-94982426 chr5:94982619-94982635
2	MAFK	chr5:94982213-94982772	Hela-S3	cervix:	n/a	n/a
3	SP1	chr5:94982125-94983249	A549	lung:	n/a	chr5:94982434-94982443 chr5:94982435-94982444 chr5:94982544-94982556 chr5:94982398-94982410 chr5:94982434-94982443 chr5:94982433-94982445 chr5:94982400-94982409 chr5:94982433-94982445 chr5:94982434-94982444 chr5:94982546-94982555 chr5:94982545-94982554 chr5:94982399-94982408 chr5:94982544-94982556 chr5:94982398-94982410 chr5:94982434-94982444
4	GATA2	chr5:94981989-94983295	SH-SY5Y	brain:	n/a	n/a
5	CTCF	chr5:94982171-94983013	GM12878	blood:	n/a	chr5:94982539-94982552
6	POLR2A	chr5:94982155-94986478	PBDE	blood:	n/a	n/a
7	JUND	chr5:94982514-94982714	HepG2	liver:	n/a	n/a
8	IRF1	chr5:94982136-94982830	K562	blood:	n/a	chr5:94982431-94982445 chr5:94982730-94982737 chr5:94982398-94982412
9	MAX	chr5:94982247-94983087	HUVEC	blood vessel:	n/a	chr5:94982920-94982927 chr5:94982919-94982928 chr5:94982918-94982928
10	USF1	chr5:94982055-94982813	SK-N-SH	brain:	n/a	chr5:94982415-94982426 chr5:94982619-94982635
11	E2F6	chr5:94982144-94983143	H1-hESC	embryonic stem cell:	n/a	chr5:94982435-94982444 chr5:94982545-94982554 chr5:94982226-94982235 chr5:94982399-94982408
12	TCF7L2	chr5:94982172-94982729	MCF-7	breast:	n/a	n/a
13	MAX	chr5:94982029-94983319	A549	lung:	n/a	chr5:94982920-94982927 chr5:94982919-94982928 chr5:94982918-94982928
14	GATA3	chr5:94982014-94982957	A549	lung:	n/a	n/a
15	POLR2A	chr5:94982155-94983736	GM12891	blood:	n/a	n/a
16	RAD21	chr5:94982176-94982879	H1-hESC	embryonic stem cell:	n/a	chr5:94982542-94982552
17	YY1	chr5:94982265-94982810	K562	blood:	n/a	chr5:94982435-94982444 chr5:94982540-94982554 chr5:94982618-94982629
18	NR2F2	chr5:94981919-94982886	MCF-7	breast:	n/a	n/a
19	POLR2A	chr5:94982451-94983199	GM12891	blood:	n/a	n/a
20	USF1	chr5:94982106-94982790	A549	lung:	n/a	chr5:94982415-94982426 chr5:94982619-94982635
21	NR3C1	chr5:94982334-94982726	ECC-1	luminal epithelium:	n/a	chr5:94982528-94982535
22	USF1	chr5:94982123-94983089	A549	lung:	n/a	chr5:94982415-94982426 chr5:94982619-94982635
23	RCOR1	chr5:94982154-94982730	K562	blood:	n/a	n/a
24	MAX	chr5:94982138-94983177	ECC-1	luminal epithelium:	n/a	chr5:94982920-94982927 chr5:94982919-94982928 chr5:94982918-94982928
25	POLR2A	chr5:94982163-94983281	Hela-S3	cervix:	n/a	n/a
26	CREB1	chr5:94982231-94983059	A549	lung:	n/a	n/a
27	USF1	chr5:94982053-94982847	HCT-116	colon:	n/a	chr5:94982415-94982426 chr5:94982619-94982635
28	JUND	chr5:94982249-94982845	A549	lung:	n/a	n/a
29	RUNX3	chr5:94982329-94983260	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:94982276-94983300	MCF-7	breast:	n/a	n/a
31	ZBTB7A	chr5:94982443-94982728	HepG2	liver:	n/a	n/a
32	POLR2A	chr5:94982116-94983123	HCT-116	colon:	n/a	n/a
33	POLR2A	chr5:94982155-94983161	GM12878	blood:	n/a	n/a
34	CTCF	chr5:94982640-94982790	A549	lung:	n/a	n/a
35	POLR2A	chr5:94982277-94982979	GM12892	blood:	n/a	n/a
36	CTCF	chr5:94982620-94982770	HA-sp	spinal cord:	n/a	n/a
37	YY1	chr5:94982416-94982975	K562	blood:	n/a	chr5:94982435-94982444 chr5:94982540-94982554 chr5:94982618-94982629
38	MYC	chr5:94982168-94983253	NB4	blood:	n/a	chr5:94982920-94982927 chr5:94982919-94982928 chr5:94982918-94982928
39	ZEB1	chr5:94982345-94983100	GM12878	blood:	n/a	chr5:94982740-94982749
40	HDAC2	chr5:94982414-94982800	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr5:94982396-94982973	Hela-S3	cervix:	n/a	n/a
42	BCLAF1	chr5:94982264-94983085	K562	blood:	n/a	chr5:94982617-94982630 chr5:94982576-94982589 chr5:94982849-94982862 chr5:94982616-94982629
43	USF1	chr5:94982110-94982730	A549	lung:	n/a	chr5:94982415-94982426 chr5:94982619-94982635
44	POLR2A	chr5:94982154-94983028	U87	brain:	n/a	n/a
45	TEAD4	chr5:94982088-94983239	K562	blood:	n/a	n/a
46	MXI1	chr5:94982290-94983101	H1-hESC	embryonic stem cell:	n/a	chr5:94982918-94982927 chr5:94982416-94982425
47	EBF1	chr5:94982410-94982826	GM12878	blood:	n/a	n/a
48	MAFK	chr5:94982307-94982779	HepG2	liver:	n/a	n/a
49	SIN3AK20	chr5:94982459-94982739	K562	blood:	n/a	n/a
50	TAF1	chr5:94982294-94982970	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:94982685-94982735	ProgFib	skin:	n/a
2	chr5:94982685-94982735	GM12891	blood:	n/a
3	chr5:94982685-94982735	MCF-7	breast:	n/a
4	chr5:94982685-94982735	AG04449	skin:	fetal
5	chr5:94982685-94982735	AG09309	skin:	n/a
6	chr5:94982685-94982735	K562	blood:	n/a
7	chr5:94982685-94982735	NH-A	brain:	n/a
8	chr5:94982685-94982735	PANC-1	pancreas:	n/a
9	chr5:94982685-94982735	IMR90	lung:	fetal
10	chr5:94982685-94982735	HMEC	breast:	n/a
11	chr5:94982685-94982735	Jurkat	blood:	n/a
12	chr5:94982685-94982735	NHDF-neo	bronchial:	n/a
13	chr5:94982685-94982735	MCF10A-Er-Src	breast:	n/a
14	chr5:94982685-94982735	U87	brain:	n/a
15	chr5:94982685-94982735	GM19239	blood:	n/a
16	chr5:94982685-94982735	Hepatocyte	liver:	n/a
17	chr5:94982685-94982735	HRCEpiC	kidney:	n/a
18	chr5:94982685-94982735	HCF	heart:	n/a
19	chr5:94982685-94982735	HCM	heart:	n/a
20	chr5:94982685-94982735	SK-N-MC	brain:	n/a
21	chr5:94982685-94982735	GM06990	blood:	n/a
22	chr5:94982685-94982735	Hela-S3	cervix:	n/a
23	chr5:94982685-94982735	BE2_C	brain:	n/a
24	chr5:94982685-94982735	CMK	blood:	n/a
25	chr5:94982685-94982735	SK-N-SH	brain:	n/a
26	chr5:94982685-94982735	AG10803	skin:	n/a
27	chr5:94982685-94982735	AoSMC	blood vessel:	n/a
28	chr5:94982685-94982735	H1-hESC	embryonic stem cell:	embryo
29	chr5:94982685-94982735	AG04450	lung:	fetal
30	chr5:94982685-94982735	GM12892	blood:	n/a
31	chr5:94982685-94982735	HCT-116	colon:	n/a
32	chr5:94982685-94982735	HUVEC	blood vessel:	n/a
33	chr5:94982685-94982735	HRE	kidney:	n/a
34	chr5:94982685-94982735	NT2-D1	testis:	n/a
35	chr5:94982685-94982735	SK-N-SH_RA	brain:	n/a
36	chr5:94982685-94982735	Caco-2	colon:	n/a
37	chr5:94982685-94982735	SKMC	muscle:	n/a
38	chr5:94982685-94982735	HEEpiC	esophagus:	n/a
39	chr5:94982685-94982735	HIPEpiC	eye:	n/a
40	chr5:94982685-94982735	AG09319	gingival:	n/a
41	chr5:94982685-94982735	NHBE	bronchial:	n/a
42	chr5:94982685-94982735	PFSK-1	brain:	n/a
43	chr5:94982685-94982735	HAEpiC	amniotic membrane:	n/a
44	chr5:94982685-94982735	HL-60	blood:	n/a
45	chr5:94982685-94982735	HNPCEpiC	eye:	n/a
46	chr5:94982685-94982735	HEK293	kidney:	embryo
47	chr5:94982685-94982735	BJ	skin:	n/a
48	chr5:94982685-94982735	T-47D	breast:	n/a
49	chr5:94982685-94982735	ECC-1	luminal epithelium:	n/a
50	chr5:94982685-94982735	HepG2	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:94982383..94984588-chr5:95046353..95049787,5	MCF-7	breast:
2	chr5:94981556..94984192-chr5:95101303..95104225,2	MCF-7	breast:
3	chr5:94981368..94988467-chr5:95046173..95051252,17	K562	blood:
4	chr5:94977116..95012475-chr5:95055682..95079552,215	K562	blood:
5	chr5:94982379..94987076-chr5:95045372..95049493,6	K562	blood:
6	chr5:94980512..95018354-chr5:95057997..95080764,228	K562	blood:
7	chr5:94979988..94984168-chr5:95032454..95035928,4	MCF-7	breast:
8	chr5:94888891..94893786-chr5:94981389..94987516,11	K562	blood:
9	chr5:94980020..94983633-chr5:95104411..95107623,3	K562	blood:
10	chr5:94980861..94985410-chr5:95067178..95071099,5	MCF-7	breast:
11	chr5:94889492..94895025-chr5:94981557..94985063,8	K562	blood:
12	chr5:90676216..90679010-chr5:94981409..94984145,2	K562	blood:
13	chr5:94979878..94983810-chr5:95295717..95298674,4	K562	blood:
14	chr5:94979432..94984462-chr5:95062276..95069972,15	MCF-7	breast:
15	chr5:94981340..94984731-chr5:95103817..95108133,4	K562	blood:
16	chr5:94953878..94956024-chr5:94981084..94983825,2	K562	blood:
17	chr5:94981287..94984175-chr5:95296229..95298674,3	K562	blood:
18	chr5:94981172..94985318-chr5:95169805..95176246,5	MCF-7	breast:

Variant related genes	Relation type
RFESD	TF binding region
RFESD	CpG island
ENSG00000118985	Chromatin interaction
ENSG00000164292	Chromatin interaction
ENSG00000178015	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000251314	Chromatin interaction
ENSG00000145757	Chromatin interaction
ENSG00000251000	Chromatin interaction
ENSG00000198677	Chromatin interaction
ENSG00000251348	Chromatin interaction
ENSG00000164291	Chromatin interaction
ENSG00000250240	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10063774	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13166682	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13172592	0.97[ASN][1000 genomes]
rs13179768	0.96[ASN][1000 genomes]
rs150548	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs150549	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs150550	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213507	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213510	0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213511	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213512	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213880	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213885	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213888	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411817	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412026	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs440342	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4869245	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6865873	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6890832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598955	chr5:94903453-95136019	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv598960	chr5:94975592-94988482	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs213887	RHOBTB3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94982000-94982800	Active TSS	Colonic Mucosa	Colon
2	chr5:94982000-94982800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr5:94982000-94982800	Active TSS	Hela-S3	cervix
4	chr5:94982000-94983200	Active TSS	Fetal Brain Female	brain
5	chr5:94982000-94983600	Active TSS	A549	lung
6	chr5:94982200-94982800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:94982200-94982800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr5:94982200-94982800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:94982200-94982800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr5:94982200-94982800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:94982200-94982800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:94982200-94982800	Active TSS	Adipose Nuclei	Adipose
13	chr5:94982200-94982800	Active TSS	Brain Germinal Matrix	brain
14	chr5:94982200-94982800	Active TSS	Duodenum Mucosa	Duodenum
15	chr5:94982200-94982800	Active TSS	Fetal Muscle Leg	muscle
16	chr5:94982200-94982800	Active TSS	Pancreas	Pancrea
17	chr5:94982200-94982800	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr5:94982200-94982800	Active TSS	Rectal Smooth Muscle	rectum
19	chr5:94982200-94982800	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr5:94982200-94982800	Active TSS	Stomach Smooth Muscle	stomach
21	chr5:94982200-94982800	Active TSS	HSMM	muscle
22	chr5:94982200-94982800	Active TSS	Osteobl	bone
23	chr5:94982200-94983000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr5:94982200-94983000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr5:94982200-94983000	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr5:94982200-94983000	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr5:94982200-94983000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:94982200-94983000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:94982200-94983000	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr5:94982200-94983000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:94982200-94983000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:94982200-94983000	Active TSS	Brain Anterior Caudate	brain
33	chr5:94982200-94983000	Active TSS	Brain Cingulate Gyrus	brain
34	chr5:94982200-94983000	Active TSS	Brain Hippocampus Middle	brain
35	chr5:94982200-94983000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:94982200-94983000	Active TSS	Brain Substantia Nigra	brain
37	chr5:94982200-94983000	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr5:94982200-94983000	Active TSS	Fetal Brain Male	brain
39	chr5:94982200-94983000	Active TSS	Fetal Lung	lung
40	chr5:94982200-94983000	Active TSS	HSMMtube	muscle
41	chr5:94982200-94983000	Active TSS	NHDF-Ad	bronchial
42	chr5:94982200-94983000	Active TSS	NHLF	lung
43	chr5:94982200-94983200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr5:94982200-94983200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:94982200-94983200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr5:94982200-94983200	Flanking Active TSS	Liver	Liver
47	chr5:94982200-94983200	Active TSS	Brain Angular Gyrus	brain
48	chr5:94982200-94983200	Flanking Active TSS	Placenta	Placenta
49	chr5:94982200-94983200	Active TSS	Ovary	ovary
50	chr5:94982200-94983200	Active TSS	Stomach Mucosa	stomach

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