Variant report

Variant	rs3766378
Chromosome Location	chr1:160807409-160807410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160805876..160808335-chr1:160811999..160814822,2	K562	blood:
2	chr1:160807406..160807999-chr1:160920889..160921402,2	K562	blood:
3	chr1:160802328..160804621-chr1:160806389..160808035,2	K562	blood:
4	chr1:160806018..160807839-chr1:160809156..160811151,2	K562	blood:

Variant related genes	Relation type
ENSG00000158764	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11265485	0.80[JPT][hapmap]
rs11265498	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11265500	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs12035295	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12036607	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs12036670	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs12037395	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs12037740	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12037885	0.81[JPT][hapmap]
rs12038419	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12038600	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12039896	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12039959	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12040060	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12040152	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12047127	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12048113	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1576964	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1855188	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1855189	0.86[ASN][1000 genomes]
rs3753389	0.89[YRI][hapmap]
rs4656936	0.81[AFR][1000 genomes]
rs4656940	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4656941	0.94[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4656943	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs480104	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501026	0.86[JPT][hapmap]
rs501137	0.87[JPT][hapmap]
rs540224	0.81[JPT][hapmap]
rs560681	0.86[JPT][hapmap]
rs57483437	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs575217	0.86[JPT][hapmap]
rs579589	0.85[JPT][hapmap]
rs61803263	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6427545	0.85[JPT][hapmap]
rs6656939	0.81[JPT][hapmap]
rs6691072	0.87[JPT][hapmap]
rs72710762	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7410867	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs7412693	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7412696	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7419088	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7419110	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7419145	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs955371	0.91[CHB][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3766378	CD244	Cis_1M	lymphoblastoid	RTeQTL
rs3766378	LY9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160793000-160811600	Weak transcription	Gastric	stomach
2	chr1:160803000-160807600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr1:160803200-160807600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr1:160803200-160812400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:160803600-160810000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr1:160804000-160807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:160804400-160807600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr1:160804800-160809600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:160805000-160809200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:160805000-160809400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr1:160805200-160809000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:160805400-160808000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:160805400-160808600	Enhancers	Primary hematopoietic stem cells	blood
14	chr1:160805600-160807600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr1:160805600-160808000	Enhancers	Fetal Thymus	thymus
16	chr1:160805600-160809000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:160805600-160809000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:160805600-160809200	Enhancers	Primary B cells from cord blood	blood
19	chr1:160805600-160809200	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:160805800-160807600	Enhancers	Dnd41	blood
21	chr1:160806000-160807800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:160806000-160807800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:160806000-160808400	Enhancers	HSMMtube	muscle
24	chr1:160806000-160809000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:160806200-160807800	Enhancers	Duodenum Mucosa	Duodenum
26	chr1:160806200-160808200	Enhancers	Placenta	Placenta
27	chr1:160806200-160808600	Enhancers	Spleen	Spleen
28	chr1:160806400-160808200	Enhancers	Fetal Heart	heart
29	chr1:160806400-160808400	Enhancers	Fetal Intestine Small	intestine
30	chr1:160806600-160807600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:160806600-160807600	Weak transcription	Adipose Nuclei	Adipose
32	chr1:160806600-160807600	Weak transcription	Colonic Mucosa	Colon
33	chr1:160806600-160807600	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr1:160806600-160808200	Enhancers	Fetal Muscle Leg	muscle
35	chr1:160806600-160810800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:160806800-160807600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:160806800-160807600	Enhancers	Right Atrium	heart
38	chr1:160806800-160807800	Enhancers	Fetal Muscle Trunk	muscle
39	chr1:160806800-160808200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:160806800-160808200	Enhancers	Brain Hippocampus Middle	brain
41	chr1:160806800-160809800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:160807000-160807600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:160807000-160807800	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr1:160807000-160807800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr1:160807000-160808200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:160807200-160807600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:160807200-160807600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:160807200-160808400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:160807200-160809000	Flanking Active TSS	Thymus	Thymus
50	chr1:160807200-160811000	Weak transcription	Fetal Intestine Large	intestine

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