Variant report

Variant	rs7729422
Chromosome Location	chr5:177041995-177041996
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
ENSG00000247679	Chromatin interaction
ENSG00000027847	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10045871	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078930	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479521	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11545868	0.95[EUR][1000 genomes]
rs11960689	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651744	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]
rs12656594	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28534743	0.89[EUR][1000 genomes]
rs28738071	0.82[ASW][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs335487	0.90[EUR][1000 genomes]
rs34705130	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4976703	0.97[EUR][1000 genomes]
rs6601075	0.85[CHD][hapmap]
rs6876792	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747861	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7710333	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717102	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs7731640	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9329062	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs968406	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028400-177042600	Weak transcription	Primary B cells from cord blood	blood
2	chr5:177028400-177044800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:177028400-177045800	Weak transcription	Left Ventricle	heart
4	chr5:177028400-177045800	Weak transcription	Psoas Muscle	Psoas
5	chr5:177028400-177048400	Weak transcription	NH-A	brain
6	chr5:177028600-177046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:177028600-177049000	Weak transcription	HUVEC	blood vessel
8	chr5:177028600-177053200	Weak transcription	HSMM	muscle
9	chr5:177028800-177044600	Weak transcription	GM12878-XiMat	blood
10	chr5:177029000-177054200	Weak transcription	Brain Substantia Nigra	brain
11	chr5:177029200-177045600	Weak transcription	Brain Angular Gyrus	brain
12	chr5:177032800-177045600	Weak transcription	HSMMtube	muscle
13	chr5:177033000-177045600	Weak transcription	Aorta	Aorta
14	chr5:177034400-177045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:177034400-177046200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:177034400-177048600	Weak transcription	A549	lung
17	chr5:177034600-177044400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:177034800-177044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr5:177034800-177044600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:177034800-177045000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:177034800-177052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:177035000-177043400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:177035000-177044600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:177035000-177044600	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:177035000-177044600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:177035000-177044600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:177035000-177045400	Weak transcription	Pancreas	Pancrea
28	chr5:177035000-177045400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:177035000-177045600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:177035000-177046600	Weak transcription	Fetal Brain Male	brain
31	chr5:177035000-177051000	Weak transcription	Stomach Mucosa	stomach
32	chr5:177035000-177054200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:177035200-177044400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:177035200-177044800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:177035200-177044800	Weak transcription	Fetal Kidney	kidney
36	chr5:177035200-177045600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:177035200-177053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:177035400-177044600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:177035400-177044600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:177035400-177045400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:177035800-177045600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:177035800-177045600	Weak transcription	NHEK	skin
43	chr5:177036600-177044400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:177036600-177045800	Weak transcription	Osteobl	bone
45	chr5:177036600-177048000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:177036800-177044600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:177036800-177044800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr5:177036800-177045200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr5:177037000-177042600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:177037000-177044600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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