Variant report

Variant	rs6894219
Chromosome Location	chr5:112383275-112383276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112370113..112371972-chr5:112381574..112383609,2	MCF-7	breast:
2	chr5:112256096..112258647-chr5:112382591..112384818,2	K562	blood:
3	chr5:112381725..112385379-chr5:112386016..112389315,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10039618	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs10054158	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10477486	0.85[CHB][hapmap]
rs1057474	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11749921	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13156493	0.82[JPT][hapmap]
rs13177101	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs13186334	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs13445	0.83[CHD][hapmap]
rs1363333	0.85[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1549181	0.83[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17372511	0.80[JPT][hapmap]
rs2227947	0.85[CHB][hapmap]
rs2227948	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2416300	0.83[JPT][hapmap]
rs3185733	0.81[JPT][hapmap]
rs33557	0.81[JPT][hapmap]
rs3857434	0.90[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4073358	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4073359	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4074190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075350	0.81[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4235788	0.84[CHB][hapmap]
rs4301226	0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4428399	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4463174	0.85[CHB][hapmap]
rs4599529	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705749	0.81[CHD][hapmap]
rs4705750	0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4705752	0.80[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4705755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705756	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705758	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705763	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4705767	0.92[ASN][1000 genomes]
rs4778	0.81[JPT][hapmap]
rs6594665	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6862481	0.84[CHB][hapmap]
rs6877570	0.83[EUR][1000 genomes]
rs6877769	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6893016	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6893389	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6894937	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71590730	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7701781	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs7708603	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7730767	0.85[CHB][hapmap]
rs7731890	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7732198	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs9122	0.86[CHD][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs9784647	0.81[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv15902	chr5:112369563-112410775	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1817377	chr5:112373682-112389837	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv516887	chr5:112379659-112396174	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6894219	MCC	cis	cerebellum	SCAN
rs6894219	DCP2	cis	lymphoblastoid	seeQTL
rs6894219	DCP2	cis	multi-tissue	Pritchard
rs6894219	TSLP	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112362800-112385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:112363800-112384600	Weak transcription	Aorta	Aorta
3	chr5:112363800-112386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
6	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:112364000-112389400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:112364200-112386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:112370600-112396600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:112371000-112383400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:112371400-112391400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:112371600-112394200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:112372600-112384000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:112372800-112396800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:112373000-112398800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:112373200-112399000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:112374800-112386000	Weak transcription	NHDF-Ad	bronchial
20	chr5:112374800-112386200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:112375000-112402600	Weak transcription	Pancreas	Pancrea
22	chr5:112375200-112384400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:112377400-112386400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr5:112377400-112389000	Weak transcription	Primary T cells from cord blood	blood
25	chr5:112379600-112386400	Weak transcription	Brain Angular Gyrus	brain
26	chr5:112379600-112386400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:112379600-112388800	Weak transcription	Gastric	stomach
28	chr5:112379600-112388800	Weak transcription	Spleen	Spleen
29	chr5:112379600-112399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:112379600-112424200	Weak transcription	Psoas Muscle	Psoas
31	chr5:112379800-112384800	Genic enhancers	Ovary	ovary
32	chr5:112379800-112386200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:112379800-112386400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr5:112379800-112388800	Weak transcription	Brain Substantia Nigra	brain
35	chr5:112380000-112383600	Weak transcription	Fetal Heart	heart
36	chr5:112380200-112385000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr5:112380800-112383600	Weak transcription	Lung	lung
38	chr5:112381000-112385200	Weak transcription	Fetal Lung	lung
39	chr5:112381600-112385800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:112382000-112385400	Strong transcription	Left Ventricle	heart
41	chr5:112382200-112385000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:112382400-112383600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr5:112382400-112383600	Enhancers	HSMM	muscle
44	chr5:112382400-112383800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr5:112382400-112383800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:112382400-112383800	Genic enhancers	HMEC	breast
47	chr5:112382400-112383800	Enhancers	HSMMtube	muscle
48	chr5:112382400-112384200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:112382400-112384200	Enhancers	Fetal Brain Male	brain
50	chr5:112382600-112383400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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