Variant report

Variant	rs17385878
Chromosome Location	chr1:160577156-160577157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160576697..160577384-chr8:130983681..130984391,2	MCF-7	breast:
2	chr1:160576861..160577411-chr1:160588261..160588811,2	MCF-7	breast:
3	chr1:160514285..160515083-chr1:160576553..160577497,2	K562	blood:
4	chr1:160397555..160399222-chr1:160576593..160577564,27	K562	blood:
5	chr1:160514566..160515087-chr1:160576968..160577551,2	MCF-7	breast:
6	chr1:160398536..160399043-chr1:160576628..160577489,2	MCF-7	breast:
7	chr1:160386268..160386812-chr1:160576912..160577553,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1055880	0.95[CEU][hapmap]
rs1061217	0.83[CEU][hapmap]
rs11265442	0.81[CEU][hapmap]
rs11265452	0.91[CEU][hapmap]
rs11583402	0.95[CEU][hapmap]
rs11585738	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11590035	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12144628	0.81[CEU][hapmap]
rs12402879	0.81[CEU][hapmap]
rs12728784	0.84[CEU][hapmap]
rs1394078	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151607	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs1572382	0.81[CEU][hapmap]
rs16832283	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs1726	0.90[EUR][1000 genomes]
rs17381453	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs17385337	0.87[CEU][hapmap]
rs17385407	0.96[CEU][hapmap]
rs1809963	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1998651	0.81[CEU][hapmap]
rs2025516	0.81[CEU][hapmap]
rs2083128	0.88[CEU][hapmap]
rs2099604	0.86[CEU][hapmap]
rs2753260	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs3733264	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs3733265	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs3733266	0.96[CEU][hapmap]
rs3766385	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3766387	0.96[CEU][hapmap]
rs3766388	0.87[CEU][hapmap]
rs3766389	0.96[CEU][hapmap]
rs3816146	0.88[CEU][hapmap]
rs5002947	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs55841347	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56040770	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56168064	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56367214	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61801562	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61801564	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61801565	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61801567	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802606	0.80[EUR][1000 genomes]
rs61802608	0.84[EUR][1000 genomes]
rs6662093	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668760	0.84[CEU][hapmap]
rs6670721	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6687641	0.92[CEU][hapmap]
rs6692382	0.84[CEU][hapmap]
rs67197441	0.84[EUR][1000 genomes]
rs72708832	0.84[EUR][1000 genomes]
rs7547054	0.88[CEU][hapmap]
rs7550771	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs912582	0.96[CEU][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs977019	0.84[CEU][hapmap]

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	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17385878	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160574000-160578800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:160575000-160577400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:160575000-160577600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:160575200-160577200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr1:160575200-160577400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:160575200-160577600	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:160575200-160577600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:160575200-160577600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:160575200-160577800	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:160575400-160577600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr1:160575600-160584000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:160575800-160577200	Enhancers	Primary T cells from cord blood	blood
13	chr1:160575800-160577600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:160575800-160577600	Enhancers	Dnd41	blood
15	chr1:160576000-160577400	Enhancers	Primary B cells from cord blood	blood
16	chr1:160576000-160577400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:160576000-160579000	Enhancers	Liver	Liver
18	chr1:160576000-160580200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:160576200-160577200	Enhancers	Thymus	Thymus
20	chr1:160576200-160577600	Enhancers	K562	blood
21	chr1:160576200-160591400	Weak transcription	Spleen	Spleen
22	chr1:160576400-160584800	Genic enhancers	Fetal Thymus	thymus
23	chr1:160576800-160577200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:160576800-160577400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:160576800-160591400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:160577000-160577600	Enhancers	GM12878-XiMat	blood
27	chr1:160577000-160580200	Weak transcription	Fetal Intestine Large	intestine
28	chr1:160577000-160580400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:160577000-160580800	Weak transcription	Fetal Intestine Small	intestine
30	chr1:160577000-160581000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:160577000-160584200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:160577000-160590800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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