Variant report

Variant	rs10434642
Chromosome Location	chr5:70823029-70823030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10044572	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10055460	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10060578	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10064099	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10077085	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10474383	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805884	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10942284	0.88[EUR][1000 genomes]
rs10942533	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10942682	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942700	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10942702	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10942705	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11743135	0.93[EUR][1000 genomes]
rs11746722	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12152748	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12153571	0.86[AMR][1000 genomes]
rs12514732	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12516456	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12652715	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13157835	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3748043	0.93[EUR][1000 genomes]
rs4062889	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4505929	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5005863	0.86[EUR][1000 genomes]
rs62361818	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6452722	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6452900	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6453013	0.87[EUR][1000 genomes]
rs6453014	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6453018	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453035	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6453043	0.92[AMR][1000 genomes]
rs6871148	0.84[ASN][1000 genomes]
rs6872235	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872671	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877289	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6877773	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886336	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715747	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7378662	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7380115	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7380280	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7444322	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7447726	0.88[EUR][1000 genomes]
rs7448422	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7449316	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7714527	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7715648	0.88[EUR][1000 genomes]
rs7721179	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7727576	0.88[EUR][1000 genomes]
rs7728577	0.93[EUR][1000 genomes]
rs7735544	0.86[EUR][1000 genomes]
rs9968768	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv882177	chr5:70800538-70856378	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv882178	chr5:70806958-70856378	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv882179	chr5:70807073-70856378	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10434642	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70754400-70824200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:70759800-70833400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:70777600-70837600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:70778400-70869600	Weak transcription	Stomach Mucosa	stomach
5	chr5:70789600-70825400	Weak transcription	Fetal Heart	heart
6	chr5:70796200-70825400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:70799400-70840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:70799800-70838800	Weak transcription	Spleen	Spleen
9	chr5:70801800-70839000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:70803800-70823600	Strong transcription	Fetal Muscle Leg	muscle
11	chr5:70805800-70844600	Weak transcription	Gastric	stomach
12	chr5:70806200-70831400	Weak transcription	Fetal Brain Male	brain
13	chr5:70806600-70829200	Weak transcription	Psoas Muscle	Psoas
14	chr5:70816400-70828000	Weak transcription	HMEC	breast
15	chr5:70819200-70824000	Strong transcription	Fetal Stomach	stomach
16	chr5:70820000-70839000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:70820200-70823400	Weak transcription	NHDF-Ad	bronchial
18	chr5:70820200-70824000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:70820200-70825000	Weak transcription	Lung	lung
20	chr5:70820200-70825200	Weak transcription	Fetal Lung	lung
21	chr5:70820200-70827600	Weak transcription	NHEK	skin
22	chr5:70820200-70828000	Weak transcription	Fetal Kidney	kidney
23	chr5:70820200-70828200	Weak transcription	Hela-S3	cervix
24	chr5:70820200-70828600	Weak transcription	HSMM	muscle
25	chr5:70820200-70828600	Weak transcription	NHLF	lung
26	chr5:70820200-70831400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:70820200-70831400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:70820200-70831400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:70820200-70831800	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:70820200-70831800	Weak transcription	Ovary	ovary
31	chr5:70820200-70832200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr5:70820200-70837400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr5:70820200-70838400	Weak transcription	Aorta	Aorta
34	chr5:70820200-70838800	Weak transcription	Pancreas	Pancrea
35	chr5:70820200-70838800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:70820200-70839000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:70820200-70839800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:70820200-70841200	Weak transcription	Colonic Mucosa	Colon
39	chr5:70820200-70841200	Weak transcription	Esophagus	oesophagus
40	chr5:70820200-70841200	Weak transcription	Right Ventricle	heart
41	chr5:70820200-70841400	Weak transcription	HSMMtube	muscle
42	chr5:70820200-70857400	Weak transcription	Small Intestine	intestine
43	chr5:70820400-70823200	Weak transcription	K562	blood
44	chr5:70820400-70823400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:70820400-70823400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:70820400-70824000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:70820400-70824000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:70820400-70824000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:70820400-70824200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:70820400-70825200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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