Variant report

Variant	rs7728577
Chromosome Location	chr5:70767269-70767270
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	chr5:70765660..70767925-chr5:70897951..70899548,2	K562	blood:

Variant related genes	Relation type
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10044572	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10064079	0.80[TSI][hapmap]
rs10077085	0.89[EUR][1000 genomes]
rs10434642	0.93[EUR][1000 genomes]
rs10474383	0.93[EUR][1000 genomes]
rs10805884	0.87[EUR][1000 genomes]
rs10942284	0.90[EUR][1000 genomes]
rs10942533	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10942682	0.93[EUR][1000 genomes]
rs10942700	0.87[EUR][1000 genomes]
rs10942702	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10942705	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11743135	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11746722	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12152748	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12514732	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12516456	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs13157835	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3748043	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4062889	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4505929	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5005863	0.87[EUR][1000 genomes]
rs6452722	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6452900	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6453014	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453018	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6453035	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6872235	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6872671	0.88[EUR][1000 genomes]
rs6877289	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6877773	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6886336	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6898471	0.91[EUR][1000 genomes]
rs715747	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7378662	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7380115	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7380280	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7444322	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7446049	0.81[ASN][1000 genomes]
rs7447726	0.90[EUR][1000 genomes]
rs7448422	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7714527	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7715648	0.90[EUR][1000 genomes]
rs7721179	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7727576	0.90[EUR][1000 genomes]
rs7735544	0.90[EUR][1000 genomes]
rs9968768	0.94[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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv528571	chr5:70679626-70767269	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv882176	chr5:70738250-70860665	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7728577	MCCC2	Cis_1M	lymphoblastoid	RTeQTL
rs7728577	CENPH	cis	parietal	SCAN
rs7728577	FAM169A	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70752600-70777200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:70752600-70789200	Weak transcription	Small Intestine	intestine
3	chr5:70752600-70794800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:70753000-70781400	Weak transcription	Fetal Heart	heart
5	chr5:70753400-70771800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:70753600-70777800	Weak transcription	Stomach Mucosa	stomach
7	chr5:70754200-70769600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:70754200-70815800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:70754400-70767800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:70754400-70768400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:70754400-70768400	Strong transcription	Liver	Liver
12	chr5:70754400-70768600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:70754400-70768600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:70754400-70768600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr5:70754400-70768600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:70754400-70769000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:70754400-70769200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:70754400-70769400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr5:70754400-70769600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:70754400-70770400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:70754400-70772200	Strong transcription	Dnd41	blood
22	chr5:70754400-70773200	Strong transcription	Adipose Nuclei	Adipose
23	chr5:70754400-70773600	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:70754400-70773800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr5:70754400-70774800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:70754400-70774800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:70754400-70774800	Strong transcription	Placenta	Placenta
28	chr5:70754400-70777800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:70754400-70778200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:70754400-70795800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:70754400-70807200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr5:70754400-70809800	Strong transcription	Fetal Intestine Large	intestine
33	chr5:70754400-70824200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:70754600-70768000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:70754600-70768400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:70754600-70773600	Strong transcription	Fetal Thymus	thymus
37	chr5:70754600-70774400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:70754600-70774800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr5:70754600-70820400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:70754600-70820400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:70754800-70767800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr5:70755800-70777800	Weak transcription	Psoas Muscle	Psoas
43	chr5:70758000-70768000	Strong transcription	Primary T cells from cord blood	blood
44	chr5:70759400-70768600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:70759400-70779000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr5:70759400-70780000	Weak transcription	Fetal Brain Male	brain
47	chr5:70759600-70778200	Weak transcription	NHLF	lung
48	chr5:70759800-70833400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:70760200-70770200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:70760200-70798400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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