Variant report

Variant	rs316404
Chromosome Location	chr5:43071156-43071157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43064995..43071284-chr5:43119667..43123996,15	MCF-7	breast:
2	chr5:43070103..43072247-chr5:43117148..43119199,2	K562	blood:
3	chr5:43070295..43071835-chr5:43373758..43376387,2	MCF-7	breast:
4	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000177721	Chromatin interaction
ENSG00000215068	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10064003	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs10522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10941604	0.95[JPT][hapmap]
rs10941605	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11747714	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs12697439	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13169690	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13170208	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13178479	0.81[ASN][1000 genomes]
rs1542369	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1574407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs160709	0.81[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1618891	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs1624415	0.90[CHD][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs178415	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs186324	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs2100473	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs222060	0.81[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2329994	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2329995	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2444779	0.88[YRI][hapmap]
rs2548334	0.83[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs2548350	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs2548353	0.95[JPT][hapmap];0.96[YRI][hapmap]
rs2548356	0.95[JPT][hapmap];0.92[YRI][hapmap]
rs2603295	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2603636	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2603644	0.95[JPT][hapmap];0.84[YRI][hapmap]
rs2603656	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs2882295	0.95[JPT][hapmap];0.96[YRI][hapmap]
rs309909	0.81[ASW][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs309914	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs309923	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs309924	0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs309925	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs309926	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs309927	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs309950	0.82[CHD][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs316395	0.87[ASN][1000 genomes]
rs316396	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316398	0.83[CEU][hapmap]
rs316400	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316402	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316403	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316406	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs316408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316413	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316414	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs316416	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs316419	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs316422	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3909456	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs4033115	0.81[ASN][1000 genomes]
rs4092293	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4092294	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs512921	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs515970	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs543569	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs557076	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs565761	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567884	0.83[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs613825	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs643307	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6451660	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6451661	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6451662	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6875214	0.84[ASN][1000 genomes]
rs6879130	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6892422	0.89[CHD][hapmap];0.90[JPT][hapmap]
rs724430	0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs768441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7715065	0.95[JPT][hapmap]
rs782971	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs782978	0.83[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs782984	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs903391	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs9292862	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs316404	LOC646887	cis	multi-tissue	Pritchard
rs316404	LOC643977	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43067800-43071200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:43068000-43077600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:43068200-43074200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:43068600-43071200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:43068600-43071200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:43068600-43082600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:43069000-43081400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:43069200-43071800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:43069200-43071800	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr5:43069200-43074200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:43069400-43071200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:43069400-43071200	Weak transcription	Fetal Brain Female	brain
13	chr5:43069400-43072200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:43069400-43075800	Strong transcription	Fetal Stomach	stomach
15	chr5:43069400-43082800	Weak transcription	Colonic Mucosa	Colon
16	chr5:43069400-43087400	Weak transcription	Stomach Mucosa	stomach
17	chr5:43069600-43071200	Weak transcription	Pancreas	Pancrea
18	chr5:43069600-43071200	Weak transcription	Right Atrium	heart
19	chr5:43069600-43071200	Weak transcription	NHEK	skin
20	chr5:43069600-43072400	Strong transcription	Primary T cells from cord blood	blood
21	chr5:43069600-43073200	Strong transcription	Placenta	Placenta
22	chr5:43069600-43073400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:43069600-43075200	Weak transcription	Fetal Heart	heart
24	chr5:43069600-43077000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:43069600-43080400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr5:43069600-43080400	Strong transcription	Fetal Muscle Leg	muscle
27	chr5:43069800-43071800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:43069800-43072000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:43069800-43076000	Weak transcription	GM12878-XiMat	blood
30	chr5:43070000-43071800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:43070000-43071800	Strong transcription	NHLF	lung
32	chr5:43070000-43072200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr5:43070000-43073400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:43070000-43105400	Weak transcription	HSMMtube	muscle
35	chr5:43070200-43071600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:43070200-43071600	Strong transcription	Primary hematopoietic stem cells	blood
37	chr5:43070200-43071600	Strong transcription	HepG2	liver
38	chr5:43070200-43071800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:43070200-43071800	Strong transcription	Primary B cells from cord blood	blood
40	chr5:43070200-43071800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:43070200-43071800	Strong transcription	Small Intestine	intestine
42	chr5:43070200-43071800	Strong transcription	A549	lung
43	chr5:43070200-43071800	Strong transcription	HMEC	breast
44	chr5:43070200-43072000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:43070200-43072400	Strong transcription	Fetal Intestine Large	intestine
46	chr5:43070200-43072400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr5:43070200-43073000	Strong transcription	HSMM	muscle
48	chr5:43070200-43073400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:43070200-43073600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:43070200-43077600	Strong transcription	Fetal Intestine Small	intestine

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