Variant report

Variant	rs12515554
Chromosome Location	chr5:177043007-177043008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177033386..177036225-chr5:177041437..177044197,2	MCF-7	breast:
2	chr5:177037101..177039177-chr5:177040730..177043338,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000027847	Chromatin interaction
ENSG00000247679	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11249570	0.81[CEU][hapmap]
rs11537644	0.84[ASN][1000 genomes]
rs12515264	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13169820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs13175194	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175367	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185565	0.90[EUR][1000 genomes]
rs13187467	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs189243	0.86[ASN][1000 genomes]
rs28499263	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28587776	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28693973	0.86[ASN][1000 genomes]
rs28712028	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2878523	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs337341	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs337362	0.86[ASN][1000 genomes]
rs34457379	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34582406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34708092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34857879	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36092039	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364970	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs366470	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs461163	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62398479	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72815179	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7718106	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs834549	0.86[ASN][1000 genomes]

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	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12515554	FAM153C	cis	Esophagus Muscularis	GTEx
rs12515554	B4GALT7	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028400-177044800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:177028400-177045800	Weak transcription	Left Ventricle	heart
3	chr5:177028400-177045800	Weak transcription	Psoas Muscle	Psoas
4	chr5:177028400-177048400	Weak transcription	NH-A	brain
5	chr5:177028600-177046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr5:177028600-177049000	Weak transcription	HUVEC	blood vessel
7	chr5:177028600-177053200	Weak transcription	HSMM	muscle
8	chr5:177028800-177044600	Weak transcription	GM12878-XiMat	blood
9	chr5:177029000-177054200	Weak transcription	Brain Substantia Nigra	brain
10	chr5:177029200-177045600	Weak transcription	Brain Angular Gyrus	brain
11	chr5:177032800-177045600	Weak transcription	HSMMtube	muscle
12	chr5:177033000-177045600	Weak transcription	Aorta	Aorta
13	chr5:177034400-177045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:177034400-177046200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:177034400-177048600	Weak transcription	A549	lung
16	chr5:177034600-177044400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:177034800-177044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:177034800-177044600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:177034800-177045000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:177034800-177052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:177035000-177043400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:177035000-177044600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:177035000-177044600	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:177035000-177044600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:177035000-177044600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:177035000-177045400	Weak transcription	Pancreas	Pancrea
27	chr5:177035000-177045400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:177035000-177045600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:177035000-177046600	Weak transcription	Fetal Brain Male	brain
30	chr5:177035000-177051000	Weak transcription	Stomach Mucosa	stomach
31	chr5:177035000-177054200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:177035200-177044400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr5:177035200-177044800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:177035200-177044800	Weak transcription	Fetal Kidney	kidney
35	chr5:177035200-177045600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:177035200-177053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr5:177035400-177044600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:177035400-177044600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:177035400-177045400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr5:177035800-177045600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:177035800-177045600	Weak transcription	NHEK	skin
42	chr5:177036600-177044400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:177036600-177045800	Weak transcription	Osteobl	bone
44	chr5:177036600-177048000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr5:177036800-177044600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:177036800-177044800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr5:177036800-177045200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr5:177037000-177044600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr5:177037000-177044800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:177037000-177044800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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