Variant report

Variant	rs6889184
Chromosome Location	chr5:177047425-177047426
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	chr5:177036778..177039311-chr5:177043869..177047459,3	MCF-7	breast:
2	chr5:176981357..176984003-chr5:177046420..177048337,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B4GALT7-1	chr5:177045917-177047505	NONHSAT105447

Variant related genes	Relation type
ENSG00000272459	Chromatin interaction
ENSG00000247679	Chromatin interaction
ENSG00000146067	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10036396	0.99[ASN][1000 genomes]
rs10040391	0.97[ASN][1000 genomes]
rs10063842	0.89[ASN][1000 genomes]
rs1047577	1.00[ASN][1000 genomes]
rs11249619	0.84[ASN][1000 genomes]
rs11490750	0.84[ASN][1000 genomes]
rs12654617	0.94[ASN][1000 genomes]
rs13164561	0.94[ASN][1000 genomes]
rs17832583	0.85[ASN][1000 genomes]
rs1872623	1.00[ASN][1000 genomes]
rs1872624	0.84[ASN][1000 genomes]
rs1963011	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2133716	0.91[ASN][1000 genomes]
rs2334991	0.89[ASN][1000 genomes]
rs2650285	0.89[ASN][1000 genomes]
rs28375402	0.83[ASN][1000 genomes]
rs28579790	0.83[ASN][1000 genomes]
rs28757437	0.82[ASN][1000 genomes]
rs34327383	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3965330	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4458584	0.99[ASN][1000 genomes]
rs56981142	0.90[ASN][1000 genomes]
rs59542146	0.86[ASN][1000 genomes]
rs60992195	0.82[ASN][1000 genomes]
rs6882209	1.00[ASN][1000 genomes]
rs6886539	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs729459	0.88[AFR][1000 genomes]
rs7703727	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7708299	0.90[ASN][1000 genomes]
rs7731783	0.93[ASN][1000 genomes]
rs901379	0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6889184	RP11-1101H11.1	cis	Heart Left Ventricle	GTEx
rs6889184	FAM153A	cis	Heart Left Ventricle	GTEx
rs6889184	B4GALT7	cis	Whole Blood	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028400-177048400	Weak transcription	NH-A	brain
2	chr5:177028600-177049000	Weak transcription	HUVEC	blood vessel
3	chr5:177028600-177053200	Weak transcription	HSMM	muscle
4	chr5:177029000-177054200	Weak transcription	Brain Substantia Nigra	brain
5	chr5:177034400-177048600	Weak transcription	A549	lung
6	chr5:177034800-177052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:177035000-177051000	Weak transcription	Stomach Mucosa	stomach
8	chr5:177035000-177054200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:177035200-177053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:177036600-177048000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:177037000-177055200	Weak transcription	NHLF	lung
12	chr5:177038600-177054400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr5:177039400-177051400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:177041600-177050200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr5:177041600-177054400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr5:177043000-177048800	Strong transcription	Fetal Brain Female	brain
17	chr5:177043200-177048600	Strong transcription	Adipose Nuclei	Adipose
18	chr5:177043400-177047800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:177043400-177050000	Strong transcription	Ovary	ovary
20	chr5:177043400-177052800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:177043600-177051800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:177043800-177049800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:177044000-177047800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:177044000-177047800	Strong transcription	Primary B cells from cord blood	blood
25	chr5:177044000-177047800	Strong transcription	Primary T cells from cord blood	blood
26	chr5:177044000-177051400	Weak transcription	HMEC	breast
27	chr5:177044400-177047800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:177044400-177048800	Strong transcription	Fetal Lung	lung
29	chr5:177044400-177049000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr5:177044400-177050000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:177044400-177061800	Weak transcription	Small Intestine	intestine
32	chr5:177044600-177047800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:177044600-177047800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr5:177044600-177047800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:177044600-177047800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:177044600-177047800	Strong transcription	Fetal Intestine Large	intestine
37	chr5:177044600-177048000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:177044600-177048000	Strong transcription	Brain Germinal Matrix	brain
39	chr5:177044600-177048000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr5:177044600-177049400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr5:177044600-177049800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:177044800-177047800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr5:177044800-177048000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:177044800-177048400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:177044800-177048400	Strong transcription	Thymus	Thymus
46	chr5:177044800-177049400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr5:177045000-177048600	Strong transcription	Fetal Muscle Leg	muscle
48	chr5:177045000-177050200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:177045000-177054200	Weak transcription	GM12878-XiMat	blood
50	chr5:177045200-177047800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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