Variant report

Variant	rs17083456
Chromosome Location	chr5:93447747-93447748
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	JUND	chr5:93446803-93447988	K562	blood:	n/a	n/a
2	POLR2A	chr5:93446805-93447789	U87	brain:	n/a	n/a
3	POLR2A	chr5:93447079-93447748	GM12892	blood:	n/a	n/a
4	RUNX3	chr5:93446842-93447764	GM12878	blood:	n/a	chr5:93447194-93447209
5	MYC	chr5:93446958-93447765	K562	blood:	n/a	n/a
6	HCFC1	chr5:93445990-93448092	Hela-S3	cervix:	n/a	n/a
7	TCF12	chr5:93446681-93447793	A549	lung:	n/a	n/a
8	POLR2A	chr5:93446962-93447817	HUVEC	blood vessel:	n/a	n/a
9	E2F6	chr5:93446747-93447803	H1-hESC	embryonic stem cell:	n/a	chr5:93447250-93447261 chr5:93447311-93447322
10	E2F6	chr5:93446765-93447796	A549	lung:	n/a	chr5:93447250-93447261 chr5:93447311-93447322
11	HA-E2F1	chr5:93446771-93447761	MCF-7	breast:	n/a	n/a
12	POLR2A	chr5:93447746-93447748	ProgFib	skin:	n/a	n/a
13	MXI1	chr5:93446635-93447788	GM12878	blood:	n/a	n/a
14	STAT5A	chr5:93447133-93447767	GM12878	blood:	n/a	n/a
15	BHLHE40	chr5:93446879-93448105	GM12878	blood:	n/a	n/a
16	MAX	chr5:93446842-93447754	MCF-7	breast:	n/a	n/a
17	UBTF	chr5:93447012-93447750	K562	blood:	n/a	n/a
18	MAX	chr5:93446763-93447780	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr5:93446609-93448845	MCF10A-Er-Src	breast:	n/a	n/a
20	SIN3AK20	chr5:93446737-93447749	MCF-7	breast:	n/a	n/a
21	ELF1	chr5:93446735-93447876	HCT-116	colon:	n/a	chr5:93447353-93447364 chr5:93447750-93447761 chr5:93447414-93447425 chr5:93447352-93447365 chr5:93447414-93447425 chr5:93447354-93447363 chr5:93447353-93447364
22	ELF1	chr5:93446831-93447928	HCT-116	colon:	n/a	chr5:93447353-93447364 chr5:93447750-93447761 chr5:93447414-93447425 chr5:93447352-93447365 chr5:93447414-93447425 chr5:93447354-93447363 chr5:93447353-93447364
23	POLR2A	chr5:93446678-93448499	GM12891	blood:	n/a	n/a
24	REST	chr5:93446708-93447941	H1-neurons	neurons:	n/a	chr5:93447431-93447444 chr5:93447173-93447191 chr5:93447175-93447188
25	POLR2A	chr5:93446984-93448052	NB4	blood:	n/a	n/a
26	TCF12	chr5:93447057-93447793	ECC-1	luminal epithelium:	n/a	n/a
27	RCOR1	chr5:93446850-93447781	K562	blood:	n/a	n/a
28	MXI1	chr5:93446431-93447840	IMR90	lung:	n/a	n/a
29	POLR2A	chr5:93446910-93447794	GM12892	blood:	n/a	n/a
30	CBX3	chr5:93446941-93447798	K562	blood:	n/a	n/a
31	CREB1	chr5:93447021-93447825	GM12878	blood:	n/a	n/a
32	TBL1XR1	chr5:93446820-93447858	K562	blood:	n/a	n/a
33	ELF1	chr5:93446913-93447845	SK-N-SH	brain:	n/a	chr5:93447353-93447364 chr5:93447750-93447761 chr5:93447414-93447425 chr5:93447352-93447365 chr5:93447414-93447425 chr5:93447354-93447363 chr5:93447353-93447364
34	POLR2A	chr5:93446875-93447749	MCF-7	breast:	n/a	n/a
35	RUNX3	chr5:93446992-93447805	GM12878	blood:	n/a	chr5:93447194-93447209
36	MXI1	chr5:93446034-93448181	SK-N-SH	brain:	n/a	n/a
37	HCFC1	chr5:93446987-93447755	K562	blood:	n/a	n/a
38	POLR2A	chr5:93446858-93447751	MCF-7	breast:	n/a	n/a
39	POLR2A	chr5:93446647-93447791	HepG2	liver:	n/a	n/a
40	CTCF	chr5:93447130-93447825	K562	blood:	n/a	n/a
41	SIN3AK20	chr5:93446710-93447824	MCF-7	breast:	n/a	n/a
42	ELF1	chr5:93446800-93447781	HepG2	liver:	n/a	chr5:93447353-93447364 chr5:93447750-93447761 chr5:93447414-93447425 chr5:93447352-93447365 chr5:93447414-93447425 chr5:93447354-93447363 chr5:93447353-93447364
43	POLR2A	chr5:93446921-93447829	PBDE	blood:	n/a	n/a
44	POLR2A	chr5:93446586-93447844	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr5:93446936-93448012	U87	brain:	n/a	n/a
46	POLR2A	chr5:93446878-93447783	IMR90	lung:	n/a	n/a
47	SIN3AK20	chr5:93446841-93447789	HCT-116	colon:	n/a	n/a
48	ELF1	chr5:93446890-93447750	K562	blood:	n/a	chr5:93447353-93447364 chr5:93447414-93447425 chr5:93447352-93447365 chr5:93447414-93447425 chr5:93447354-93447363 chr5:93447353-93447364
49	MYBL2	chr5:93446970-93447787	HepG2	liver:	n/a	n/a
50	PML	chr5:93446971-93447861	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:93447700-93447750	HNPCEpiC	eye:	n/a
2	chr5:93447700-93447750	H1-hESC	embryonic stem cell:	embryo
3	chr5:93447700-93447750	NB4	blood:	n/a
4	chr5:93447700-93447750	MCF10A-Er-Src	breast:	n/a
5	chr5:93447700-93447750	PFSK-1	brain:	n/a
6	chr5:93447700-93447750	IMR90	lung:	fetal
7	chr5:93447700-93447750	HCT-116	colon:	n/a
8	chr5:93447700-93447750	GM19239	blood:	n/a
9	chr5:93447700-93447750	HMEC	breast:	n/a
10	chr5:93447700-93447750	AG04450	lung:	fetal
11	chr5:93447700-93447750	NHDF-neo	bronchial:	n/a
12	chr5:93447700-93447750	AG09319	gingival:	n/a
13	chr5:93447700-93447750	GM06990	blood:	n/a
14	chr5:93447700-93447750	HRE	kidney:	n/a
15	chr5:93447700-93447750	HL-60	blood:	n/a
16	chr5:93447700-93447750	AG10803	skin:	n/a
17	chr5:93447700-93447750	RPTEC	kidney:	n/a
18	chr5:93447700-93447750	ovcar-3	ovarian:	n/a
19	chr5:93447700-93447750	HepG2	liver:	n/a
20	chr5:93447700-93447750	SAEC	small airway:	n/a
21	chr5:93447700-93447750	K562	blood:	n/a
22	chr5:93447700-93447750	NT2-D1	testis:	n/a
23	chr5:93447700-93447750	Hela-S3	cervix:	n/a
24	chr5:93447700-93447750	HAEpiC	amniotic membrane:	n/a
25	chr5:93447700-93447750	BE2_C	brain:	n/a
26	chr5:93447700-93447750	CMK	blood:	n/a
27	chr5:93447700-93447750	HPAEpiC	pulmonary alveolar:	n/a
28	chr5:93447700-93447750	AG04449	skin:	fetal
29	chr5:93447700-93447750	HUVEC	blood vessel:	n/a
30	chr5:93447700-93447750	PrEC	prostate:	n/a
31	chr5:93447700-93447750	GM12878	blood:	n/a
32	chr5:93447700-93447750	BJ	skin:	n/a
33	chr5:93447700-93447750	HCM	heart:	n/a
34	chr5:93447700-93447750	NH-A	brain:	n/a
35	chr5:93447700-93447750	SKMC	muscle:	n/a
36	chr5:93447700-93447750	GM12892	blood:	n/a
37	chr5:93447700-93447750	ECC-1	luminal epithelium:	n/a
38	chr5:93447700-93447750	U87	brain:	n/a
39	chr5:93447700-93447750	SK-N-MC	brain:	n/a
40	chr5:93447700-93447750	GM12891	blood:	n/a
41	chr5:93447700-93447750	ProgFib	skin:	n/a
42	chr5:93447700-93447750	PANC-1	pancreas:	n/a
43	chr5:93447700-93447750	Hepatocyte	liver:	n/a
44	chr5:93447700-93447750	HIPEpiC	eye:	n/a
45	chr5:93447700-93447750	Caco-2	colon:	n/a
46	chr5:93447700-93447750	SK-N-SH	brain:	n/a
47	chr5:93447700-93447750	AoSMC	blood vessel:	n/a
48	chr5:93447700-93447750	A549	lung:	n/a
49	chr5:93447700-93447750	Jurkat	blood:	n/a
50	chr5:93447700-93447750	HEK293	kidney:	embryo

No.	Distal block	Cell Line	Cell type
1	chr5:65439986..65440532-chr5:93446947..93447861,2	Hela-S3	cervix:
2	chr5:93447483..93449055-chr5:93449239..93451183,2	MCF-7	breast:
3	chr16:9184954..9185814-chr5:93446887..93447822,2	Hela-S3	cervix:
4	chr19:2456845..2457544-chr5:93447193..93447793,2	Hela-S3	cervix:
5	chr5:93447486..93450547-chr5:93454924..93457929,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANKRD32-10	chr5:93447458-93448080	NONHSAT102819

Variant related genes	Relation type
FAM172A	TF binding region
FAM172A	CpG island
ENSG00000176619	Chromatin interaction
ENSG00000182831	Chromatin interaction
ENSG00000153914	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17083426	1.00[ASW][hapmap]
rs61046714	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7701468	1.00[ASW][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap]
rs7705961	0.84[AFR][1000 genomes]
rs7721368	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532196	chr5:92933949-93573527	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1023191	chr5:93351646-93947928	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv537808	chr5:93351646-93947928	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv2753025	chr5:93356544-93812844	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv530552	chr5:93416111-93588509	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93445800-93447800	Active TSS	Primary T cells from cord blood	blood
2	chr5:93446000-93447800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:93446000-93447800	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr5:93446000-93447800	Active TSS	Fetal Kidney	kidney
5	chr5:93446000-93447800	Active TSS	Rectal Smooth Muscle	rectum
6	chr5:93446000-93448000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr5:93446000-93448000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:93446000-93448000	Active TSS	Brain Angular Gyrus	brain
9	chr5:93446000-93448000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr5:93446000-93448000	Active TSS	NHDF-Ad	bronchial
11	chr5:93446000-93448000	Active TSS	NHLF	lung
12	chr5:93446000-93448200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:93446200-93447800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:93446200-93447800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:93446200-93447800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:93446200-93447800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:93446200-93448000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:93446200-93448000	Active TSS	Brain Hippocampus Middle	brain
19	chr5:93446200-93448000	Active TSS	Stomach Smooth Muscle	stomach
20	chr5:93446200-93448200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:93446200-93448200	Active TSS	Colon Smooth Muscle	Colon
22	chr5:93446200-93448400	Active TSS	Brain Substantia Nigra	brain
23	chr5:93446400-93447800	Active TSS	H1 Cell Line	embryonic stem cell
24	chr5:93446400-93447800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:93446400-93447800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr5:93446400-93447800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:93446400-93447800	Active TSS	Brain Cingulate Gyrus	brain
28	chr5:93446400-93447800	Active TSS	Fetal Intestine Small	intestine
29	chr5:93446400-93447800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr5:93446400-93447800	Active TSS	Fetal Thymus	thymus
31	chr5:93446400-93447800	Active TSS	Ovary	ovary
32	chr5:93446400-93447800	Active TSS	Placenta Amnion	Placenta Amnion
33	chr5:93446400-93447800	Active TSS	Right Ventricle	heart
34	chr5:93446400-93448000	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr5:93446400-93448000	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr5:93446400-93448000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr5:93446400-93448000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr5:93446400-93448000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:93446400-93448000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:93446400-93448000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr5:93446400-93448000	Active TSS	Fetal Muscle Leg	muscle
42	chr5:93446400-93448000	Active TSS	Psoas Muscle	Psoas
43	chr5:93446400-93448000	Active TSS	GM12878-XiMat	blood
44	chr5:93446400-93448200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:93446400-93448200	Active TSS	Brain Anterior Caudate	brain
46	chr5:93446400-93448200	Active TSS	K562	blood
47	chr5:93446600-93447800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:93446600-93447800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr5:93446600-93447800	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr5:93446600-93447800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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