Variant report

Variant	rs17471
Chromosome Location	chr3:119817673-119817674
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:9)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr3:119817619-119817863	T-47D	breast:	n/a	n/a
2	POLR2A	chr3:119817554-119817796	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:119817403-119818170	K562	blood:	n/a	n/a
4	GATA3	chr3:119817505-119817866	MCF-7	breast:	n/a	chr3:119817675-119817683
5	GATA3	chr3:119817332-119818043	MCF-7	breast:	n/a	chr3:119817675-119817683
6	POLR2A	chr3:119817372-119818059	H1-hESC	embryonic stem cell:	n/a	n/a
7	ESR1	chr3:119817553-119817857	T-47D	breast:	n/a	n/a
8	POLR2A	chr3:119817222-119818032	HepG2	liver:	n/a	n/a
9	TCF12	chr3:119817444-119817883	MCF-7	breast:	n/a	n/a
10	POLR2A	chr3:119817503-119818360	HepG2	liver:	n/a	n/a
11	EP300	chr3:119817459-119817896	MCF-7	breast:	n/a	n/a
12	SIN3AK20	chr3:119817230-119818179	MCF-7	breast:	n/a	n/a
13	TCF7L2	chr3:119817587-119817920	MCF-7	breast:	n/a	n/a
14	POLR2A	chr3:119817491-119818368	MCF10A-Er-Src	breast:	n/a	n/a
15	GATA3	chr3:119817391-119817976	MCF-7	breast:	n/a	chr3:119817675-119817683
16	POLR2A	chr3:119817502-119817821	MCF10A-Er-Src	breast:	n/a	n/a
17	HDAC2	chr3:119817460-119817981	MCF-7	breast:	n/a	n/a
18	ZNF217	chr3:119817480-119818036	MCF-7	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119817451..119819097-chr3:119825949..119828864,2	K562	blood:
2	chr3:119817665..119819771-chr3:120066591..120068812,2	MCF-7	breast:
3	chr3:119816323..119819155-chr3:119879849..119882520,2	MCF-7	breast:
4	chr3:119655041..119657977-chr3:119815420..119818415,2	K562	blood:
5	chr3:119816356..119819205-chr3:119850914..119853051,2	MCF-7	breast:
6	chr3:119817098..119817801-chr3:119865724..119866308,2	MCF-7	breast:
7	chr3:119816888..119819583-chr3:119917638..119919426,2	MCF-7	breast:
8	chr3:119817292..119818147-chr3:120068347..120068875,2	MCF-7	breast:
9	chr3:119776406..119778250-chr3:119816051..119818083,2	MCF-7	breast:

(count:9 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1I2-1	chr3:119817561-119817826	XLOC_002779
2	lnc-NR1I2-1	chr3:119817561-119819241	XLOC_002779
3	lnc-NR1I2-1	chr3:119817561-119817826	XLOC_002779
4	lnc-NR1I2-1	chr3:119817561-119817826	XLOC_002779
5	lnc-NR1I2-1	chr3:119817561-119817826	XLOC_002779
6	lnc-NR1I2-1	chr3:119817561-119818033	ENSG00000242622
7	lnc-NR1I2-1	chr3:119813266-119819259	NONHSAT091417
8	lnc-NR1I2-1	chr3:119817561-119817826	NONHSAT091425
9	lnc-NR1I2-1	chr3:119817561-119819230	XLOC_002779

No data

Variant related genes	Relation type
GSK3B	TF binding region
ENSG00000163428	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11719490	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs334555	0.81[AMR][1000 genomes]

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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119814600-119830600	Weak transcription	Gastric	stomach
2	chr3:119815000-119818000	Enhancers	Small Intestine	intestine
3	chr3:119815000-119829200	Weak transcription	Ovary	ovary
4	chr3:119815200-119819000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:119815200-119822000	Weak transcription	Esophagus	oesophagus
6	chr3:119815400-119817800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr3:119815400-119818400	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:119815400-119819600	Weak transcription	Primary T cells from cord blood	blood
9	chr3:119815400-119819600	Weak transcription	HSMMtube	muscle
10	chr3:119815400-119821000	Weak transcription	Adipose Nuclei	Adipose
11	chr3:119815400-119821000	Weak transcription	NH-A	brain
12	chr3:119815400-119821600	Weak transcription	Psoas Muscle	Psoas
13	chr3:119815400-119828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:119815400-119828200	Weak transcription	Aorta	Aorta
15	chr3:119815400-119828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:119815400-119830000	Weak transcription	Fetal Lung	lung
17	chr3:119815600-119820600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:119815600-119821200	Weak transcription	Fetal Kidney	kidney
19	chr3:119815600-119826000	Weak transcription	Primary B cells from cord blood	blood
20	chr3:119815800-119819400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:119815800-119819400	Weak transcription	NHLF	lung
22	chr3:119815800-119829000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:119816000-119817800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:119816000-119817800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:119816000-119818400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:119816000-119818400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:119816000-119819800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:119816000-119819800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:119816000-119820200	Weak transcription	Brain Germinal Matrix	brain
30	chr3:119816000-119821000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:119816000-119821000	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:119816000-119821200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:119816000-119821600	Weak transcription	Fetal Stomach	stomach
34	chr3:119816000-119821600	Weak transcription	Left Ventricle	heart
35	chr3:119816000-119821600	Weak transcription	Lung	lung
36	chr3:119816000-119821600	Weak transcription	Right Atrium	heart
37	chr3:119816000-119821600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:119816000-119822200	Weak transcription	Right Ventricle	heart
39	chr3:119816000-119822400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:119816000-119827400	Weak transcription	Thymus	Thymus
41	chr3:119816000-119828600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:119816000-119829000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:119816200-119820400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:119816200-119821600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:119816200-119821600	Weak transcription	Pancreas	Pancrea
46	chr3:119816200-119823200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:119816200-119831000	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:119816200-119832600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:119816400-119819000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:119816400-119819200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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