Variant report

Variant	rs6600989
Chromosome Location	chr5:177044707-177044708
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	chr5:177038565..177041096-chr5:177043118..177044821,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B4GALT7-1	chr5:177044449-177045805	NONHSAT105447

Variant related genes	Relation type
ENSG00000247679	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11249570	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs13169820	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs13175194	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs13175367	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs1963011	0.87[AFR][1000 genomes]
rs34582406	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs6600992	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729459	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][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
rs6600989	B4GALT7	cis	Whole Blood	GTEx
rs6600989	B4GALT7	cis	lymphoblastoid	seeQTL
rs6600989	RP11-1277A3.2	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 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	chr5:177029000-177054200	Weak transcription	Brain Substantia Nigra	brain
9	chr5:177029200-177045600	Weak transcription	Brain Angular Gyrus	brain
10	chr5:177032800-177045600	Weak transcription	HSMMtube	muscle
11	chr5:177033000-177045600	Weak transcription	Aorta	Aorta
12	chr5:177034400-177045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:177034400-177046200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:177034400-177048600	Weak transcription	A549	lung
15	chr5:177034800-177045000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:177034800-177052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:177035000-177045400	Weak transcription	Pancreas	Pancrea
18	chr5:177035000-177045400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:177035000-177045600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:177035000-177046600	Weak transcription	Fetal Brain Male	brain
21	chr5:177035000-177051000	Weak transcription	Stomach Mucosa	stomach
22	chr5:177035000-177054200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:177035200-177044800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:177035200-177044800	Weak transcription	Fetal Kidney	kidney
25	chr5:177035200-177045600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:177035200-177053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:177035400-177045400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:177035800-177045600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:177035800-177045600	Weak transcription	NHEK	skin
30	chr5:177036600-177045800	Weak transcription	Osteobl	bone
31	chr5:177036600-177048000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:177036800-177044800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr5:177036800-177045200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:177037000-177044800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:177037000-177044800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:177037000-177045200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr5:177037000-177045400	Weak transcription	Gastric	stomach
38	chr5:177037000-177045800	Weak transcription	Fetal Thymus	thymus
39	chr5:177037000-177055200	Weak transcription	NHLF	lung
40	chr5:177037200-177045000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:177037200-177045200	Weak transcription	Esophagus	oesophagus
42	chr5:177037200-177045400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr5:177037200-177045600	Weak transcription	Colonic Mucosa	Colon
44	chr5:177037200-177046000	Weak transcription	Right Ventricle	heart
45	chr5:177037200-177047400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:177037400-177045200	Weak transcription	Liver	Liver
47	chr5:177037600-177045400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr5:177037800-177045400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:177037800-177046200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:177038000-177045800	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links