Variant report

Variant	rs2120200
Chromosome Location	chr17:38460375-38460376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38458898..38461237-chr17:38499745..38502287,2	K562	blood:
2	chr17:38267756..38269556-chr17:38459898..38462579,2	K562	blood:
3	chr17:38288101..38290586-chr17:38457763..38460423,2	K562	blood:
4	chr17:38457066..38460899-chr17:38504442..38513119,13	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDC6-1	chr17:38459457-38460909	ENSG00000270145.1

Variant related genes	Relation type
ENSG00000131759	Chromatin interaction
ENSG00000188895	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11078940	0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs12051734	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12103711	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12946680	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13706	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16965687	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs1807273	0.92[ASN][1000 genomes]
rs2077464	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2280400	0.87[GIH][hapmap]
rs28537537	0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs35286757	0.88[ASN][1000 genomes]
rs36030243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077125	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs4134994	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4566234	0.80[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap]
rs55656553	0.96[ASN][1000 genomes]
rs57179137	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59406133	0.86[ASN][1000 genomes]
rs6503539	0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap]
rs7217852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs7359537	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs8066144	0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs9303285	0.81[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.91[ASN][1000 genomes]
rs9303286	0.80[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9892946	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs9893520	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs9894625	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9896312	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9904021	0.81[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap]
rs9904270	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.95[ASN][1000 genomes]
rs9908034	0.84[CHB][hapmap]
rs9916460	0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs9916782	0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38444800-38462600	Weak transcription	Esophagus	oesophagus
2	chr17:38445600-38462600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:38446000-38461000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:38450800-38461200	Strong transcription	Dnd41	blood
5	chr17:38452600-38460800	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr17:38452600-38461000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:38452800-38461400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr17:38452800-38461400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr17:38453000-38461000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:38453000-38462600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr17:38453400-38461200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:38455800-38462800	Weak transcription	Ovary	ovary
13	chr17:38456600-38460600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:38456600-38460800	Strong transcription	GM12878-XiMat	blood
15	chr17:38459000-38460800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
16	chr17:38459000-38461200	Genic enhancers	HMEC	breast
17	chr17:38459000-38461800	Enhancers	NHLF	lung
18	chr17:38459000-38462400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr17:38459000-38465400	Enhancers	Fetal Muscle Leg	muscle
20	chr17:38459000-38465400	Enhancers	Fetal Stomach	stomach
21	chr17:38459200-38460600	Enhancers	Liver	Liver
22	chr17:38459200-38460600	Genic enhancers	A549	lung
23	chr17:38459200-38460800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr17:38459200-38461000	Genic enhancers	NHEK	skin
25	chr17:38459200-38461400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr17:38459200-38461600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:38459200-38462800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:38459200-38465200	Enhancers	Fetal Intestine Large	intestine
29	chr17:38459200-38465400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr17:38459200-38473800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr17:38459400-38460400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr17:38459400-38460400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr17:38459400-38460400	Genic enhancers	Thymus	Thymus
34	chr17:38459400-38460400	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr17:38459400-38460600	Enhancers	Primary T cells from cord blood	blood
36	chr17:38459400-38460600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr17:38459400-38460600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr17:38459400-38460600	Enhancers	Brain Substantia Nigra	brain
39	chr17:38459400-38460600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr17:38459400-38460600	Enhancers	Spleen	Spleen
41	chr17:38459400-38460600	Genic enhancers	Hela-S3	cervix
42	chr17:38459400-38460600	Enhancers	HUVEC	blood vessel
43	chr17:38459400-38460800	Enhancers	Primary hematopoietic stem cells	blood
44	chr17:38459400-38460800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr17:38459400-38460800	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr17:38459400-38460800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:38459400-38460800	Enhancers	Duodenum Mucosa	Duodenum
48	chr17:38459400-38460800	Enhancers	Fetal Heart	heart
49	chr17:38459400-38461000	Genic enhancers	Fetal Thymus	thymus
50	chr17:38459400-38461200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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