Variant report

Variant	rs57985907
Chromosome Location	chr3:98244170-98244171
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr3:98240387-98245434	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:98243267-98244808	GM12891	blood:	n/a	n/a
3	WRNIP1	chr3:98243931-98244679	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:98242436-98244841	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:98240046-98245016	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:98240411-98244872	GM12891	blood:	n/a	n/a
7	POU2F2	chr3:98244013-98244842	GM12878	blood:	n/a	chr3:98244713-98244728 chr3:98244717-98244732 chr3:98244711-98244726
8	RUNX3	chr3:98244158-98244823	GM12878	blood:	n/a	chr3:98244560-98244569 chr3:98244560-98244569
9	POLR2A	chr3:98243948-98245002	GM19193	blood:	n/a	n/a
10	RUNX3	chr3:98244129-98244955	GM12878	blood:	n/a	chr3:98244560-98244569 chr3:98244560-98244569
11	PML	chr3:98240482-98245009	GM12878	blood:	n/a	chr3:98244546-98244554 chr3:98241150-98241159 chr3:98242731-98242739
12	POLR2A	chr3:98239998-98244935	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:98240336-98244846	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:98243849-98244764	GM12878	blood:	n/a	n/a
15	MTA3	chr3:98243274-98244836	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:98240432-98245015	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:98244013-98244234	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:98239707-98244952	GM12891	blood:	n/a	n/a
19	POLR2A	chr3:98243966-98244668	GM12878	blood:	n/a	n/a
20	NFIC	chr3:98243477-98245065	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:98240313-98245042	GM12892	blood:	n/a	n/a
22	STAT5A	chr3:98243362-98244768	GM12878	blood:	n/a	chr3:98244438-98244446
23	NFATC1	chr3:98240005-98244929	GM12878	blood:	n/a	n/a
24	POU2F2	chr3:98243958-98244672	GM12891	blood:	n/a	n/a
25	POLR2A	chr3:98243995-98244699	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:98240501-98244890	GM19099	blood:	n/a	n/a
27	POLR2A	chr3:98239743-98248227	GM12878	blood:	n/a	n/a
28	BCLAF1	chr3:98243929-98244818	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:98240472-98244893	GM12892	blood:	n/a	n/a
30	POLR2A	chr3:98239894-98245276	GM18505	blood:	n/a	n/a
31	POLR2A	chr3:98239775-98244942	GM12891	blood:	n/a	n/a
32	POLR2A	chr3:98240882-98244693	GM15510	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:98244170-98244220	RPTEC	kidney:	n/a
2	chr3:98244170-98244220	GM12878	blood:	n/a
3	chr3:98244170-98244220	IMR90	lung:	fetal
4	chr3:98244170-98244220	AG09309	skin:	n/a
5	chr3:98244170-98244220	AG04449	skin:	fetal
6	chr3:98244170-98244220	HUVEC	blood vessel:	n/a
7	chr3:98244170-98244220	PFSK-1	brain:	n/a
8	chr3:98244170-98244220	Caco-2	colon:	n/a
9	chr3:98244170-98244220	ovcar-3	ovarian:	n/a
10	chr3:98244170-98244220	NHDF-neo	bronchial:	n/a
11	chr3:98244170-98244220	Hepatocyte	liver:	n/a
12	chr3:98244170-98244220	NB4	blood:	n/a
13	chr3:98244170-98244220	NH-A	brain:	n/a
14	chr3:98244170-98244220	SK-N-MC	brain:	n/a
15	chr3:98244170-98244220	MCF-7	breast:	n/a
16	chr3:98244170-98244220	A549	lung:	n/a
17	chr3:98244170-98244220	U87	brain:	n/a
18	chr3:98244170-98244220	HPAEpiC	pulmonary alveolar:	n/a
19	chr3:98244170-98244220	HRPEpiC	eye:	n/a
20	chr3:98244170-98244220	HEEpiC	esophagus:	n/a
21	chr3:98244170-98244220	ECC-1	luminal epithelium:	n/a
22	chr3:98244170-98244220	LNCaP	prostate:	n/a
23	chr3:98244170-98244220	SKMC	muscle:	n/a
24	chr3:98244170-98244220	HepG2	liver:	n/a
25	chr3:98244170-98244220	SK-N-SH	brain:	n/a
26	chr3:98244170-98244220	HCPEpiC	choroid plexus:	n/a
27	chr3:98244170-98244220	HEK293	kidney:	embryo
28	chr3:98244170-98244220	T-47D	breast:	n/a
29	chr3:98244170-98244220	GM12892	blood:	n/a
30	chr3:98244170-98244220	PrEC	prostate:	n/a
31	chr3:98244170-98244220	HCM	heart:	n/a
32	chr3:98244170-98244220	CMK	blood:	n/a
33	chr3:98244170-98244220	AG10803	skin:	n/a
34	chr3:98244170-98244220	Hela-S3	cervix:	n/a
35	chr3:98244170-98244220	H1-hESC	embryonic stem cell:	embryo
36	chr3:98244170-98244220	GM06990	blood:	n/a
37	chr3:98244170-98244220	NHBE	bronchial:	n/a
38	chr3:98244170-98244220	HL-60	blood:	n/a
39	chr3:98244170-98244220	HAEpiC	amniotic membrane:	n/a
40	chr3:98244170-98244220	HRCEpiC	kidney:	n/a
41	chr3:98244170-98244220	Jurkat	blood:	n/a
42	chr3:98244170-98244220	SK-N-SH_RA	brain:	n/a
43	chr3:98244170-98244220	PANC-1	pancreas:	n/a
44	chr3:98244170-98244220	HNPCEpiC	eye:	n/a
45	chr3:98244170-98244220	HCF	heart:	n/a
46	chr3:98244170-98244220	ProgFib	skin:	n/a
47	chr3:98244170-98244220	HRE	kidney:	n/a
48	chr3:98244170-98244220	SAEC	small airway:	n/a
49	chr3:98244170-98244220	BJ	skin:	n/a
50	chr3:98244170-98244220	NT2-D1	testis:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98241176..98243261-chr3:98243368..98246193,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR15-1	chr3:98244055-98244178	ENSG00000248839.1

No data

Variant related genes	Relation type
CLDND1	TF binding region
RPL38P4	TF binding region
CLDND1	CpG island
RPL38P4	CpG island
ENSG00000080822	Chromatin interaction
ENSG00000248839	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1471299	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16839839	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16839882	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16846235	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1961152	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56787128	1.00[EUR][1000 genomes]
rs58755405	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58756404	1.00[EUR][1000 genomes]
rs59248577	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60788607	1.00[EUR][1000 genomes]
rs61642998	1.00[EUR][1000 genomes]
rs7626745	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834774	chr3:98108423-98274064	Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98241800-98244200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:98241800-98244600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:98241800-98246800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:98242200-98246800	Weak transcription	Fetal Intestine Large	intestine
5	chr3:98242200-98247200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:98242200-98250800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:98242400-98244200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:98242400-98244400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:98242400-98244400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:98242400-98244400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:98242400-98244400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:98242400-98244400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:98242400-98247200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:98242800-98247400	Weak transcription	K562	blood
15	chr3:98243000-98247600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
16	chr3:98243600-98244600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:98244000-98244600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:98244000-98244800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:98244000-98244800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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