Variant report

Variant	rs375782190
Chromosome Location	chr3:49508535-49508536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:49506252-49509681	SK-N-SH	brain:	n/a	n/a
2	SIN3A	chr3:49506507-49508607	H1-hESC	embryonic stem cell:	n/a	chr3:49507507-49507520 chr3:49506954-49506963 chr3:49507546-49507557
3	CTCF	chr3:49508400-49508550	GM12872	blood:	n/a	n/a
4	RAD21	chr3:49507857-49508793	IMR90	lung:	n/a	n/a
5	HCFC1	chr3:49506744-49509311	Hela-S3	cervix:	n/a	n/a
6	REST	chr3:49506809-49508612	H1-neurons	neurons:	n/a	chr3:49507579-49507592 chr3:49507507-49507520
7	RCOR1	chr3:49506525-49508730	IMR90	lung:	n/a	n/a
8	RELA	chr3:49507144-49508756	GM10847	blood:	n/a	n/a
9	MTA3	chr3:49507568-49508639	GM12878	blood:	n/a	n/a
10	STAT5A	chr3:49507587-49508541	GM12878	blood:	n/a	n/a
11	FOXA1	chr3:49508126-49508576	HepG2	liver:	n/a	chr3:49508357-49508372
12	POLR2A	chr3:49506525-49508693	K562	blood:	n/a	n/a
13	KAP1	chr3:49506587-49508751	HEK293	kidney:	n/a	n/a
14	POLR2A	chr3:49507046-49508756	PBDE	blood:	n/a	n/a
15	TCF12	chr3:49506772-49508580	ECC-1	luminal epithelium:	n/a	chr3:49506823-49506833 chr3:49508362-49508371
16	FOXA1	chr3:49508179-49508556	T-47D	breast:	n/a	chr3:49508357-49508372
17	PML	chr3:49506842-49508569	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:49506311-49508860	H1-hESC	embryonic stem cell:	n/a	n/a
19	MXI1	chr3:49506448-49509224	IMR90	lung:	n/a	n/a
20	CHD1	chr3:49508478-49508783	GM12878	blood:	n/a	n/a
21	MXI1	chr3:49506536-49508628	Hela-S3	cervix:	n/a	n/a
22	MAZ	chr3:49506361-49509347	IMR90	lung:	n/a	chr3:49507013-49507023 chr3:49509096-49509107

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49506494..49510419-chr3:49709515..49713189,4	MCF-7	breast:
2	chr3:49507792..49509395-chr3:49538517..49540372,2	MCF-7	breast:
3	chr3:49506988..49509379-chr3:49529279..49532110,2	MCF-7	breast:
4	chr3:49506481..49509131-chr3:49546764..49549304,2	MCF-7	breast:
5	chr3:49447402..49451449-chr3:49505916..49509646,7	K562	blood:
6	chr3:49506444..49509653-chr3:49710909..49714606,3	K562	blood:
7	chr3:49056423..49060378-chr3:49506507..49510634,4	K562	blood:
8	chr3:49447402..49452044-chr3:49506038..49509646,9	K562	blood:
9	chr16:30536975..30539864-chr3:49506980..49509217,2	MCF-7	breast:
10	chr3:49501861..49505109-chr3:49505439..49508808,5	K562	blood:
11	chr3:49130007..49132020-chr3:49507888..49509693,2	K562	blood:
12	chr3:49448236..49450769-chr3:49505936..49509558,3	MCF-7	breast:
13	chr3:49448736..49451146-chr3:49507489..49509395,2	MCF-7	breast:
14	chr3:49460325..49461920-chr3:49506460..49509220,2	MCF-7	breast:
15	chr3:49503012..49504721-chr3:49506646..49509185,2	MCF-7	breast:
16	chr3:49507807..49509484-chr3:49555798..49559257,3	MCF-7	breast:
17	chr3:49507938..49509712-chr3:49512685..49515016,2	K562	blood:
18	chr3:49376524..49378988-chr3:49507303..49509521,2	MCF-7	breast:
19	chr3:49508269..49511222-chr3:49551619..49554342,2	K562	blood:
20	chr3:49455358..49458192-chr3:49507443..49509538,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP130	TF binding region
ENSG00000169957	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000201301	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000145020	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3420339	chr3:49505548-49510046	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv3439400	chr3:49506373-49508921	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3380038	chr3:49506748-49508796	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49506400-49509200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49506400-49509600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr3:49506800-49508600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:49506800-49508800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:49506800-49509200	Active TSS	Psoas Muscle	Psoas
6	chr3:49507000-49508600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:49507000-49508600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:49507000-49508600	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:49507000-49508600	Active TSS	Fetal Kidney	kidney
10	chr3:49507000-49508800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:49507000-49508800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:49507000-49508800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:49507000-49508800	Active TSS	Lung	lung
14	chr3:49507000-49508800	Active TSS	Ovary	ovary
15	chr3:49507000-49509000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:49507000-49509000	Active TSS	Aorta	Aorta
17	chr3:49507000-49509000	Active TSS	A549	lung
18	chr3:49507200-49508600	Active TSS	H1 Cell Line	embryonic stem cell
19	chr3:49507200-49508600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:49507200-49508600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:49507200-49508600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr3:49507200-49508600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:49507200-49508600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:49507200-49508600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr3:49507200-49508600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:49507200-49508600	Active TSS	Brain Substantia Nigra	brain
27	chr3:49507200-49508600	Active TSS	Colon Smooth Muscle	Colon
28	chr3:49507200-49508600	Active TSS	Duodenum Mucosa	Duodenum
29	chr3:49507200-49508600	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr3:49507200-49508600	Active TSS	Fetal Brain Female	brain
31	chr3:49507200-49508600	Active TSS	Fetal Intestine Large	intestine
32	chr3:49507200-49508600	Active TSS	Fetal Stomach	stomach
33	chr3:49507200-49508600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr3:49507200-49508600	Active TSS	GM12878-XiMat	blood
35	chr3:49507200-49508800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr3:49507200-49508800	Active TSS	Esophagus	oesophagus
37	chr3:49507200-49508800	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr3:49507200-49508800	Active TSS	Small Intestine	intestine
39	chr3:49507200-49509000	Active TSS	Fetal Intestine Small	intestine
40	chr3:49507200-49509200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:49507200-49509200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:49507200-49509200	Active TSS	Left Ventricle	heart
43	chr3:49507400-49508600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:49507400-49508600	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr3:49507400-49508600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:49507400-49508600	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr3:49507400-49508600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:49507400-49508600	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr3:49507400-49508600	Active TSS	Placenta	Placenta
50	chr3:49507400-49508600	Active TSS	Rectal Smooth Muscle	rectum

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