Variant report

Variant	rs480104
Chromosome Location	chr1:160801046-160801047
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160696291..160697336-chr1:160800205..160801082,4	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11265485	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs11265498	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11265500	0.82[CHB][hapmap]
rs12035295	0.81[CHB][hapmap]
rs12037740	0.80[ASN][1000 genomes]
rs12038600	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12039896	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12039959	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12040060	0.81[ASN][1000 genomes]
rs12040152	0.85[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs12047127	0.80[ASN][1000 genomes]
rs12048113	0.86[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1576964	0.80[ASN][1000 genomes]
rs1855188	0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2139660	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs34002161	0.82[ASN][1000 genomes]
rs3766378	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656940	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4656941	0.81[ASN][1000 genomes]
rs501026	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs501137	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs506263	0.82[ASN][1000 genomes]
rs520316	0.86[ASN][1000 genomes]
rs527253	0.86[ASN][1000 genomes]
rs540224	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs560681	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs57483437	0.80[ASN][1000 genomes]
rs575217	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs579589	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6427545	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs6656939	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6691072	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7412693	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs7412696	0.80[ASN][1000 genomes]
rs7419088	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7419110	0.86[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7419145	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7555286	0.85[CEU][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs480104	LY9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160771000-160806600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:160782600-160803200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:160783800-160803200	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr1:160790600-160803000	Strong transcription	Primary T cells from cord blood	blood
5	chr1:160793000-160811600	Weak transcription	Gastric	stomach
6	chr1:160793400-160807400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:160794000-160805800	Weak transcription	Thymus	Thymus
8	chr1:160794000-160806200	Weak transcription	Spleen	Spleen
9	chr1:160794200-160803000	Weak transcription	Fetal Thymus	thymus
10	chr1:160796800-160804800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:160797200-160805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:160797600-160805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:160797600-160805200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:160797800-160805600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:160798200-160803000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:160798200-160804600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:160798200-160805000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:160798200-160805000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:160798200-160805000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:160798200-160805600	Weak transcription	Primary B cells from cord blood	blood
21	chr1:160798400-160805000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:160798600-160805600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:160799000-160805200	Strong transcription	Primary hematopoietic stem cells	blood
24	chr1:160800000-160803200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:160800200-160803000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:160800800-160801400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:160800800-160803200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:160800800-160803400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:160800800-160805800	Weak transcription	GM12878-XiMat	blood
30	chr1:160801000-160803600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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