Variant report

Variant	rs6554097
Chromosome Location	chr4:54232644-54232645
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	GATA1	chr4:54230902-54233271	K562	blood:	n/a	chr4:54233253-54233262
2	POLR2A	chr4:54231483-54232749	PBDE	blood:	n/a	n/a
3	SIN3AK20	chr4:54231615-54232719	MCF-7	breast:	n/a	n/a
4	HCFC1	chr4:54231070-54232843	Hela-S3	cervix:	n/a	n/a
5	ZNF143	chr4:54232118-54232684	K562	blood:	n/a	n/a
6	JUND	chr4:54231987-54232734	K562	blood:	n/a	chr4:54232160-54232168
7	JUN	chr4:54231199-54233391	K562	blood:	n/a	chr4:54233236-54233244 chr4:54232160-54232168
8	MAZ	chr4:54231887-54232666	GM12878	blood:	n/a	chr4:54232209-54232222 chr4:54232210-54232221 chr4:54232366-54232382 chr4:54232212-54232221
9	MYBL2	chr4:54231937-54232862	HepG2	liver:	n/a	n/a
10	MXI1	chr4:54230837-54232923	IMR90	lung:	n/a	chr4:54232212-54232221
11	GATA3	chr4:54231994-54232736	MCF-7	breast:	n/a	n/a
12	MAZ	chr4:54231918-54232685	K562	blood:	n/a	chr4:54232209-54232222 chr4:54232210-54232221 chr4:54232366-54232382 chr4:54232212-54232221
13	ZMIZ1	chr4:54231899-54232691	K562	blood:	n/a	n/a
14	POLR2A	chr4:54231147-54233099	GM12891	blood:	n/a	n/a
15	POLR2A	chr4:54231313-54232823	K562	blood:	n/a	n/a
16	MAX	chr4:54231654-54232658	A549	lung:	n/a	chr4:54232209-54232222 chr4:54232210-54232221 chr4:54232366-54232382 chr4:54232212-54232221
17	POLR2A	chr4:54231807-54232778	GM12878	blood:	n/a	n/a
18	RUNX3	chr4:54231657-54232653	GM12878	blood:	n/a	n/a
19	EP300	chr4:54232087-54232699	GM12878	blood:	n/a	n/a
20	RCOR1	chr4:54232079-54232776	GM12878	blood:	n/a	n/a
21	ELK4	chr4:54231295-54232667	Hela-S3	cervix:	n/a	chr4:54232164-54232175
22	POLR2A	chr4:54231553-54233049	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr4:54232089-54232896	K562	blood:	n/a	n/a
24	WRNIP1	chr4:54232021-54232689	GM12878	blood:	n/a	n/a
25	TBP	chr4:54232016-54232819	Hela-S3	cervix:	n/a	n/a
26	SETDB1	chr4:54232113-54232849	U2OS	brain:	n/a	n/a
27	SP1	chr4:54231887-54232703	HCT-116	colon:	n/a	chr4:54232263-54232284 chr4:54232329-54232339 chr4:54232328-54232340 chr4:54232329-54232339
28	MYC	chr4:54232012-54232767	MCF10A-Er-Src	breast:	n/a	chr4:54232209-54232222 chr4:54232210-54232221 chr4:54232366-54232382 chr4:54232212-54232221
29	RUNX3	chr4:54231645-54232760	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:54231278-54232816	GM19099	blood:	n/a	n/a
31	POLR2A	chr4:54231279-54232932	NB4	blood:	n/a	n/a
32	POLR2A	chr4:54231801-54232680	HepG2	liver:	n/a	n/a
33	NFATC1	chr4:54232022-54232784	GM12878	blood:	n/a	n/a
34	MTA3	chr4:54232206-54232727	GM12878	blood:	n/a	n/a
35	POLR2A	chr4:54231884-54232715	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr4:54232007-54232732	HCT-116	colon:	n/a	n/a
37	CHD1	chr4:54232074-54232746	GM12878	blood:	n/a	n/a
38	MYBL2	chr4:54231967-54232656	HepG2	liver:	n/a	n/a
39	POLR2A	chr4:54231245-54232673	ProgFib	skin:	n/a	n/a
40	POLR2A	chr4:54231704-54232666	GM12878	blood:	n/a	n/a
41	POLR2A	chr4:54231444-54232756	GM19193	blood:	n/a	n/a
42	POLR2A	chr4:54231614-54232655	MCF-7	breast:	n/a	n/a
43	SIN3AK20	chr4:54231619-54232817	MCF-7	breast:	n/a	n/a
44	MAX	chr4:54231324-54232653	SK-N-SH	brain:	n/a	chr4:54232209-54232222 chr4:54232210-54232221 chr4:54232366-54232382 chr4:54232212-54232221
45	CUX1	chr4:54231765-54232973	K562	blood:	n/a	n/a
46	CEBPB	chr4:54232052-54232819	GM12878	blood:	n/a	chr4:54232274-54232282
47	POLR2A	chr4:54231287-54232787	K562	blood:	n/a	n/a
48	CCNT2	chr4:54232024-54232689	K562	blood:	n/a	n/a
49	POLR2A	chr4:54231283-54232753	Raji	blood:	n/a	n/a
50	CHD2	chr4:54231957-54232839	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:54232638-54232688	Caco-2	colon:	n/a
2	chr4:54232638-54232688	MCF-7	breast:	n/a
3	chr4:54232638-54232688	PANC-1	pancreas:	n/a
4	chr4:54232638-54232688	LNCaP	prostate:	n/a
5	chr4:54232638-54232688	HCT-116	colon:	n/a
6	chr4:54232638-54232688	U87	brain:	n/a
7	chr4:54232638-54232688	Hela-S3	cervix:	n/a
8	chr4:54232638-54232688	Hepatocyte	liver:	n/a
9	chr4:54232638-54232688	HIPEpiC	eye:	n/a
10	chr4:54232638-54232688	GM12892	blood:	n/a
11	chr4:54232638-54232688	HepG2	liver:	n/a
12	chr4:54232638-54232688	GM19239	blood:	n/a
13	chr4:54232638-54232688	HPAEpiC	pulmonary alveolar:	n/a
14	chr4:54232638-54232688	HNPCEpiC	eye:	n/a
15	chr4:54232638-54232688	ProgFib	skin:	n/a
16	chr4:54232638-54232688	ECC-1	luminal epithelium:	n/a
17	chr4:54232638-54232688	Jurkat	blood:	n/a
18	chr4:54232638-54232688	HCPEpiC	choroid plexus:	n/a
19	chr4:54232638-54232688	HEK293	kidney:	embryo
20	chr4:54232638-54232688	IMR90	lung:	fetal
21	chr4:54232638-54232688	SK-N-MC	brain:	n/a
22	chr4:54232638-54232688	AG09319	gingival:	n/a
23	chr4:54232638-54232688	A549	lung:	n/a
24	chr4:54232638-54232688	NB4	blood:	n/a
25	chr4:54232638-54232688	AG10803	skin:	n/a
26	chr4:54232638-54232688	PFSK-1	brain:	n/a
27	chr4:54232638-54232688	CMK	blood:	n/a
28	chr4:54232638-54232688	K562	blood:	n/a
29	chr4:54232638-54232688	GM12878	blood:	n/a
30	chr4:54232638-54232688	NHBE	bronchial:	n/a
31	chr4:54232638-54232688	HRCEpiC	kidney:	n/a
32	chr4:54232638-54232688	HUVEC	blood vessel:	n/a
33	chr4:54232638-54232688	NT2-D1	testis:	n/a
34	chr4:54232638-54232688	AG04449	skin:	fetal
35	chr4:54232638-54232688	AoSMC	blood vessel:	n/a
36	chr4:54232638-54232688	AG09309	skin:	n/a
37	chr4:54232638-54232688	GM06990	blood:	n/a
38	chr4:54232638-54232688	NHDF-neo	bronchial:	n/a
39	chr4:54232638-54232688	H1-hESC	embryonic stem cell:	embryo
40	chr4:54232638-54232688	T-47D	breast:	n/a
41	chr4:54232638-54232688	SK-N-SH	brain:	n/a
42	chr4:54232638-54232688	BJ	skin:	n/a
43	chr4:54232638-54232688	SAEC	small airway:	n/a
44	chr4:54232638-54232688	HRE	kidney:	n/a
45	chr4:54232638-54232688	SKMC	muscle:	n/a
46	chr4:54232638-54232688	HCM	heart:	n/a
47	chr4:54232638-54232688	GM12891	blood:	n/a
48	chr4:54232638-54232688	MCF10A-Er-Src	breast:	n/a
49	chr4:54232638-54232688	HMEC	breast:	n/a
50	chr4:54232638-54232688	HCF	heart:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196669127..196670018-chr4:54231923..54232709,2	Hela-S3	cervix:
2	chr4:54231262..54233846-chr4:54243717..54245288,2	MCF-7	breast:
3	chr4:54230756..54233682-chr4:54240977..54245711,5	MCF-7	breast:
4	chr4:53585131..53587206-chr4:54232522..54234735,2	MCF-7	breast:

Variant related genes	Relation type
SCFD2	TF binding region
SCFD2	CpG island
ENSG00000248375	Chromatin interaction
ENSG00000270170	Chromatin interaction
ENSG00000114503	Chromatin interaction
ENSG00000145216	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10002674	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10006662	0.91[YRI][hapmap]
rs10010450	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10032378	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs11133259	0.87[ASW][hapmap];1.00[LWK][hapmap]
rs12507175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13137917	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13150432	1.00[YRI][hapmap]
rs1471596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2117598	0.84[YRI][hapmap]
rs2128104	0.82[YRI][hapmap]
rs2137896	0.84[AFR][1000 genomes]
rs4864462	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4864463	0.84[YRI][hapmap]
rs4864465	0.84[YRI][hapmap]
rs4864764	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4864768	0.86[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4864769	0.84[YRI][hapmap]
rs4864775	0.84[YRI][hapmap]
rs6554088	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6554101	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6821777	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6823086	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6824775	1.00[YRI][hapmap]
rs6841529	0.91[YRI][hapmap]
rs6847795	0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6850629	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6856534	0.91[YRI][hapmap]
rs7656204	0.82[YRI][hapmap]
rs7687290	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7697807	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs900113	0.81[YRI][hapmap]
rs9684941	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54224800-54233000	Active TSS	GM12878-XiMat	blood
2	chr4:54230000-54232800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr4:54230000-54232800	Active TSS	A549	lung
4	chr4:54230400-54232800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr4:54230400-54233000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:54230600-54233000	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr4:54230600-54233000	Active TSS	Fetal Kidney	kidney
8	chr4:54230600-54233000	Active TSS	HSMM	muscle
9	chr4:54230800-54232800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:54230800-54233000	Active TSS	Ovary	ovary
11	chr4:54230800-54233000	Active TSS	Psoas Muscle	Psoas
12	chr4:54230800-54233000	Active TSS	Right Atrium	heart
13	chr4:54230800-54233000	Active TSS	HSMMtube	muscle
14	chr4:54230800-54233200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr4:54231000-54233000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:54231000-54233000	Active TSS	Fetal Intestine Small	intestine
17	chr4:54231200-54232800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:54231200-54232800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:54231200-54232800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr4:54231200-54232800	Active TSS	Left Ventricle	heart
21	chr4:54231200-54232800	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr4:54231200-54233000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:54231400-54232800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr4:54231400-54232800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr4:54231400-54232800	Active TSS	Stomach Mucosa	stomach
26	chr4:54231400-54233000	Active TSS	Osteobl	bone
27	chr4:54231400-54233200	Active TSS	Colon Smooth Muscle	Colon
28	chr4:54231600-54232800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:54231600-54232800	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr4:54231600-54232800	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr4:54231600-54232800	Active TSS	Brain Cingulate Gyrus	brain
32	chr4:54231600-54232800	Active TSS	Brain Germinal Matrix	brain
33	chr4:54231600-54232800	Active TSS	Esophagus	oesophagus
34	chr4:54231600-54233000	Active TSS	Aorta	Aorta
35	chr4:54231600-54233000	Active TSS	Fetal Brain Male	brain
36	chr4:54231600-54233000	Active TSS	Fetal Brain Female	brain
37	chr4:54231600-54233000	Active TSS	Fetal Muscle Leg	muscle
38	chr4:54231600-54233000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr4:54231800-54232800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr4:54231800-54232800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:54231800-54232800	Active TSS	Brain Anterior Caudate	brain
42	chr4:54231800-54232800	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr4:54231800-54232800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:54231800-54232800	Active TSS	Fetal Muscle Trunk	muscle
45	chr4:54231800-54232800	Active TSS	Placenta Amnion	Placenta Amnion
46	chr4:54231800-54233000	Active TSS	Colonic Mucosa	Colon
47	chr4:54231800-54233000	Active TSS	Fetal Lung	lung
48	chr4:54231800-54233000	Active TSS	Right Ventricle	heart
49	chr4:54231800-54233400	Active TSS	Brain Hippocampus Middle	brain
50	chr4:54232000-54232800	Active TSS	Primary T cells fromperipheralblood	blood

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