Variant report

Variant	rs542138370
Chromosome Location	chr17:38277167-38277168
allele	C/G
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	POLR2A	chr17:38277122-38279074	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr17:38277161-38278442	PANC-1	pancreas:	n/a	n/a
3	REST	chr17:38276918-38281234	H1-neurons	neurons:	n/a	chr17:38277546-38277559 chr17:38277832-38277845
4	TCF12	chr17:38277112-38278606	A549	lung:	n/a	n/a
5	MXI1	chr17:38276962-38281499	SK-N-SH	brain:	n/a	chr17:38277801-38277816
6	MAX	chr17:38277095-38280963	A549	lung:	n/a	n/a
7	POLR2A	chr17:38277139-38280351	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr17:38277104-38280152	MCF-7	breast:	n/a	n/a
9	YY1	chr17:38277063-38279397	SK-N-SH	brain:	n/a	chr17:38278141-38278150 chr17:38278243-38278254 chr17:38278138-38278152 chr17:38277826-38277840 chr17:38277477-38277489 chr17:38278239-38278253 chr17:38277768-38277777 chr17:38277472-38277491 chr17:38278654-38278663 chr17:38277766-38277777 chr17:38278138-38278147 chr17:38277480-38277488
10	POLR2A	chr17:38275179-38278647	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr17:38277065-38278030	U87	brain:	n/a	n/a
12	MXI1	chr17:38277049-38281505	IMR90	lung:	n/a	chr17:38277801-38277816
13	POLR2A	chr17:38277040-38278030	U87	brain:	n/a	n/a
14	POLR2A	chr17:38277107-38279973	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr17:38277129-38280098	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr17:38277166-38279164	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr17:38276843-38280747	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38207226..38209173-chr17:38275974..38278338,2	K562	blood:
2	chr17:38276987..38281156-chr17:38471490..38477166,7	MCF-7	breast:
3	chr17:38274376..38281367-chr17:38331383..38338006,23	MCF-7	breast:
4	chr17:38275824..38279709-chr17:38496937..38502326,5	K562	blood:
5	chr17:38276248..38278417-chr17:38373940..38377017,3	MCF-7	breast:
6	chr17:38178218..38182497-chr17:38276428..38279757,5	MCF-7	breast:
7	chr17:38255433..38258713-chr17:38276171..38280451,4	K562	blood:
8	chr17:38223441..38229037-chr17:38277080..38281500,5	MCF-7	breast:
9	chr17:38252517..38259251-chr17:38276179..38282890,16	MCF-7	breast:
10	chr17:38276983..38277924-chr6:31587852..31588427,2	Hela-S3	cervix:
11	chr17:38276870..38280410-chr17:38295018..38299576,8	K562	blood:
12	chr17:38218404..38220452-chr17:38276626..38279762,4	K562	blood:
13	chr17:38274785..38277489-chr17:38323556..38326542,2	MCF-7	breast:
14	chr17:38276815..38279338-chr17:38332365..38335401,3	MCF-7	breast:
15	chr17:38218404..38220452-chr17:38276626..38279762,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1D1-1	chr17:38276065-38277620	XLOC_012467
2	lnc-NR1D1-1	chr17:38277006-38277663	XLOC_012467
3	lnc-NR1D1-1	chr17:38275466-38277989	NONHSAT053517

Variant related genes	Relation type
MSL1	TF binding region
ENSG00000265666	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000171475	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000108349	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000126351	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	nsv908221	chr17:38216522-38289003	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv528369	chr17:38256693-38289003	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	esv3405142	chr17:38277051-38279599	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38270200-38277200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:38270400-38277200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:38270400-38277200	Weak transcription	Primary T cells from cord blood	blood
4	chr17:38270400-38277400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:38271600-38277400	Weak transcription	Pancreas	Pancrea
6	chr17:38271800-38277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr17:38274800-38277400	Weak transcription	Small Intestine	intestine
8	chr17:38276200-38277200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:38276200-38277200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:38276200-38277200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr17:38276400-38277200	Enhancers	Esophagus	oesophagus
12	chr17:38276400-38277200	Enhancers	Placenta	Placenta
13	chr17:38276400-38277200	Enhancers	Left Ventricle	heart
14	chr17:38276400-38277200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr17:38276400-38277400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr17:38276400-38277400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr17:38276400-38277400	Enhancers	Colonic Mucosa	Colon
18	chr17:38276400-38277400	Enhancers	Psoas Muscle	Psoas
19	chr17:38276400-38277800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr17:38276400-38277800	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr17:38276600-38277200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr17:38276600-38277200	Enhancers	Primary hematopoietic stem cells	blood
23	chr17:38276600-38277200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr17:38276600-38277200	Enhancers	Aorta	Aorta
25	chr17:38276600-38277200	Enhancers	Liver	Liver
26	chr17:38276600-38277200	Enhancers	Brain Substantia Nigra	brain
27	chr17:38276600-38277200	Flanking Active TSS	Fetal Heart	heart
28	chr17:38276600-38277200	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr17:38276600-38277200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr17:38276600-38277200	Enhancers	Right Atrium	heart
31	chr17:38276600-38277200	Enhancers	Thymus	Thymus
32	chr17:38276600-38277200	Enhancers	Dnd41	blood
33	chr17:38276600-38277200	Enhancers	K562	blood
34	chr17:38276600-38277200	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr17:38276600-38277400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr17:38276600-38277400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr17:38276600-38277400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr17:38276600-38277400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr17:38276600-38277400	Weak transcription	Gastric	stomach
40	chr17:38276600-38277400	Enhancers	Spleen	Spleen
41	chr17:38276600-38277400	Flanking Active TSS	Osteobl	bone
42	chr17:38276600-38277600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:38276600-38277600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:38276600-38277600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr17:38276600-38277600	Flanking Active TSS	HMEC	breast
46	chr17:38276600-38277600	Flanking Active TSS	NHEK	skin
47	chr17:38276600-38277800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr17:38276600-38277800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr17:38276600-38280400	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr17:38276800-38277200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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