Variant report

Variant	rs4687569
Chromosome Location	chr3:51432895-51432896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51431727..51434714-chr3:51452155..51454713,2	K562	blood:
2	chr3:51432016..51433899-chr3:51699483..51701969,2	MCF-7	breast:
3	chr3:51428575..51432934-chr3:51531325..51537191,8	K562	blood:
4	chr3:51431570..51433213-chr3:51447794..51449393,2	K562	blood:
5	chr3:50652754..50655473-chr3:51429609..51433416,3	MCF-7	breast:
6	chr3:51432446..51436234-chr3:51447600..51449947,3	MCF-7	breast:
7	chr3:51430737..51433070-chr3:51447893..51450283,2	K562	blood:
8	chr3:51429653..51435090-chr3:51454270..51458499,6	MCF-7	breast:
9	chr3:51431316..51433012-chr3:51532838..51535046,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction
ENSG00000145041	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1031925	0.92[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1055429	0.90[AMR][1000 genomes]
rs10865970	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130293	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11721253	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1383251	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1383252	1.00[CHB][hapmap]
rs1480353	0.92[CEU][hapmap]
rs1480354	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1480358	0.86[CHB][hapmap]
rs1480363	0.86[CHB][hapmap]
rs1542574	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs1552072	0.86[CHB][hapmap]
rs1552073	0.86[CHB][hapmap]
rs1552074	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051734	0.85[CHB][hapmap]
rs17051762	0.84[CEU][hapmap];0.88[CHD][hapmap]
rs2061951	0.86[CHB][hapmap]
rs2127655	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2219890	0.92[CEU][hapmap]
rs2355934	0.86[CHB][hapmap]
rs2355941	0.86[CHB][hapmap]
rs4301044	0.86[CHB][hapmap]
rs4317086	0.85[AFR][1000 genomes]
rs4355273	0.80[AFR][1000 genomes]
rs4611808	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687568	0.83[AMR][1000 genomes]
rs4687721	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs4687734	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4974095	0.86[CHB][hapmap]
rs4974104	0.92[CEU][hapmap]
rs4974105	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974106	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445551	0.86[CHB][hapmap]
rs6445620	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6445622	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs6445628	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6772668	0.81[EUR][1000 genomes]
rs6773260	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6775666	0.80[AFR][1000 genomes]
rs6787312	0.85[AFR][1000 genomes]
rs6793900	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6809080	0.86[CHB][hapmap]
rs6809155	0.84[AMR][1000 genomes]
rs7372658	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs751075	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7619584	0.85[CHB][hapmap]
rs7625006	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628533	0.86[CHB][hapmap]
rs7644957	0.86[CHB][hapmap]
rs7648012	0.84[CEU][hapmap]
rs922612	0.86[CHB][hapmap]
rs9311469	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9855442	0.84[CHB][hapmap]
rs9858412	0.86[CHB][hapmap]
rs9869123	1.00[CHB][hapmap]
rs9878100	0.86[CHB][hapmap]
rs9883739	0.86[CHB][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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS 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	53 gene(s)	inside rSNPs	diseases
4	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4687569	HEMK1	cis	cerebellum	SCAN
rs4687569	TEX264	cis	Esophagus Muscularis	GTEx
rs4687569	TEX264	cis	Artery Tibial	GTEx
rs4687569	NCKIPSD	cis	cerebellum	SCAN
rs4687569	IQCF2	cis	parietal	SCAN
rs4687569	MST1	cis	cerebellum	SCAN
rs4687569	PARP3	cis	parietal	SCAN
rs4687569	TEX264	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51429600-51435000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:51430000-51433000	Enhancers	Right Atrium	heart
3	chr3:51430000-51433200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:51430000-51433200	Genic enhancers	Brain Inferior Temporal Lobe	brain
5	chr3:51430000-51433200	Genic enhancers	Placenta	Placenta
6	chr3:51430000-51433600	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr3:51430000-51434000	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr3:51430000-51434000	Genic enhancers	Fetal Stomach	stomach
9	chr3:51430000-51434200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:51430000-51434200	Genic enhancers	Gastric	stomach
11	chr3:51430000-51434400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:51430000-51434400	Genic enhancers	Spleen	Spleen
13	chr3:51430000-51435200	Genic enhancers	Left Ventricle	heart
14	chr3:51430000-51435200	Genic enhancers	Lung	lung
15	chr3:51430200-51433000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr3:51430200-51433200	Genic enhancers	Fetal Lung	lung
17	chr3:51430200-51433400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:51430200-51434000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:51430200-51434000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:51430200-51434000	Genic enhancers	Colon Smooth Muscle	Colon
21	chr3:51430200-51434200	Genic enhancers	Fetal Muscle Leg	muscle
22	chr3:51430200-51434200	Genic enhancers	HUVEC	blood vessel
23	chr3:51430200-51435200	Genic enhancers	Adipose Nuclei	Adipose
24	chr3:51430200-51437000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr3:51430200-51437200	Strong transcription	Aorta	Aorta
26	chr3:51430200-51457000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:51430400-51433200	Genic enhancers	Brain Angular Gyrus	brain
28	chr3:51430400-51433400	Genic enhancers	Primary T cells from cord blood	blood
29	chr3:51430400-51434000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:51430400-51434000	Genic enhancers	Pancreas	Pancrea
31	chr3:51430400-51434200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:51430400-51434600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:51430400-51435200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:51430400-51437200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:51430400-51438000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:51430400-51438200	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr3:51430400-51440400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:51430600-51433400	Strong transcription	Primary hematopoietic stem cells	blood
39	chr3:51430600-51433800	Genic enhancers	Duodenum Mucosa	Duodenum
40	chr3:51430600-51434600	Genic enhancers	Right Ventricle	heart
41	chr3:51430600-51435000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:51430600-51435200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:51430600-51436400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:51430600-51441200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:51430800-51433600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:51430800-51433800	Genic enhancers	NH-A	brain
47	chr3:51430800-51434200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:51430800-51435000	Strong transcription	A549	lung
49	chr3:51430800-51443200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:51431000-51433000	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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