Variant report

Variant	rs1901187
Chromosome Location	chr17:38646147-38646148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38644489..38646400-chr17:38673085..38675357,2	K562	blood:
2	chr17:38640863..38643911-chr17:38644729..38647819,3	MCF-7	breast:
3	chr17:38646024..38649623-chr17:38649808..38652805,4	K562	blood:
4	chr17:38643110..38644639-chr17:38644908..38646867,2	MCF-7	breast:
5	chr17:38600534..38602477-chr17:38644496..38646702,2	K562	blood:
6	chr17:38632398..38634313-chr17:38645464..38649244,3	MCF-7	breast:
7	chr17:38646147..38648547-chr17:38673997..38676989,2	MCF-7	breast:
8	chr17:38645169..38647955-chr17:38652977..38654925,2	K562	blood:
9	chr17:38597960..38600391-chr17:38643714..38646429,2	MCF-7	breast:
10	chr17:38640983..38649598-chr17:38652430..38659338,11	MCF-7	breast:
11	chr17:38642192..38648064-chr17:38648142..38651157,5	K562	blood:
12	chr17:38645404..38649775-chr17:38650279..38653252,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000131746	Chromatin interaction
ENSG00000141753	Chromatin interaction
ENSG00000266088	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12942610	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2290206	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2290207	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34377860	1.00[ASN][1000 genomes]
rs34453034	1.00[ASN][1000 genomes]
rs34456044	1.00[ASN][1000 genomes]
rs34879399	1.00[ASN][1000 genomes]
rs35260012	1.00[ASN][1000 genomes]
rs3764424	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7214311	0.84[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs8079359	0.82[ASW][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes]
rs8081819	1.00[ASN][1000 genomes]
rs9303289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058185	chr17:38629339-38689908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv908224	chr17:38638251-38651447	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1901187	C17orf50	cis	parietal	SCAN
rs1901187	ERBB2	cis	parietal	SCAN
rs1901187	MLLT6	cis	parietal	SCAN
rs1901187	IGFBP4	cis	cerebellum	SCAN
rs1901187	CCL13	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38627400-38646200	Weak transcription	Gastric	stomach
2	chr17:38636000-38647000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr17:38636000-38648200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr17:38636000-38649600	Genic enhancers	HMEC	breast
5	chr17:38637400-38648200	Genic enhancers	NHEK	skin
6	chr17:38638200-38646400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr17:38638600-38646200	Weak transcription	Colonic Mucosa	Colon
8	chr17:38640800-38646400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr17:38641000-38646600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:38641000-38648800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr17:38641200-38646200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:38641200-38646400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:38641400-38646200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:38642000-38647000	Enhancers	Colon Smooth Muscle	Colon
15	chr17:38642000-38647800	Enhancers	Fetal Stomach	stomach
16	chr17:38642000-38654400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr17:38642800-38646600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:38643000-38647000	Weak transcription	Fetal Kidney	kidney
19	chr17:38643000-38654200	Weak transcription	Stomach Mucosa	stomach
20	chr17:38643200-38646400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr17:38643200-38646600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr17:38643200-38647000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:38643400-38646200	Weak transcription	HepG2	liver
24	chr17:38643400-38646200	Weak transcription	K562	blood
25	chr17:38643400-38648200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr17:38643600-38646200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr17:38643600-38646400	Weak transcription	Adipose Nuclei	Adipose
28	chr17:38643800-38646200	Weak transcription	NH-A	brain
29	chr17:38643800-38656000	Weak transcription	Right Atrium	heart
30	chr17:38644000-38646400	Genic enhancers	Hela-S3	cervix
31	chr17:38644000-38648600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:38644200-38646200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr17:38644200-38646200	Genic enhancers	A549	lung
34	chr17:38644200-38646400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr17:38644200-38648400	Enhancers	Fetal Thymus	thymus
36	chr17:38644400-38646200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:38644400-38646200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr17:38644400-38646200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr17:38644400-38646200	Weak transcription	Pancreas	Pancrea
40	chr17:38644400-38646200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr17:38644400-38646200	Weak transcription	HSMMtube	muscle
42	chr17:38644400-38646200	Weak transcription	NHDF-Ad	bronchial
43	chr17:38644400-38646200	Weak transcription	NHLF	lung
44	chr17:38644400-38646400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr17:38644400-38646400	Weak transcription	Fetal Muscle Leg	muscle
46	chr17:38644400-38646400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr17:38644400-38646600	Weak transcription	Right Ventricle	heart
48	chr17:38644400-38646600	Enhancers	Stomach Smooth Muscle	stomach
49	chr17:38644400-38646600	Weak transcription	HSMM	muscle
50	chr17:38644400-38648200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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