Variant report

Variant	rs10001651
Chromosome Location	chr4:151071888-151071889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:151065674..151068783-chr4:151069402..151072348,3	MCF-7	breast:
2	chr4:151057757..151060556-chr4:151069534..151071946,2	MCF-7	breast:
3	chr4:151066204..151068081-chr4:151071216..151073291,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10001645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029811	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10033999	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10520059	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11735949	0.80[CEU][hapmap]
rs12019295	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13435185	0.80[CEU][hapmap]
rs17026748	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs2305980	0.84[CEU][hapmap]
rs28361896	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28377256	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28501175	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28598870	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605560	0.83[EUR][1000 genomes]
rs28616626	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28635652	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28673979	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4353883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59085186	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60526300	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62338190	0.80[EUR][1000 genomes]
rs62338194	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62338212	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62338216	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72732403	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7438777	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7662296	0.80[CEU][hapmap]
rs7662896	0.80[CEU][hapmap]
rs9884239	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9884665	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9997755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10001651	TIGD4	cis	parietal	SCAN
rs10001651	DCLK2	cis	Whole Blood	GTEx
rs10001651	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151045200-151099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:151049200-151074000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:151062800-151072000	Weak transcription	Aorta	Aorta
4	chr4:151064600-151080200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:151067400-151074200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:151067800-151074200	Weak transcription	HSMM	muscle
7	chr4:151068000-151074000	Weak transcription	Brain Substantia Nigra	brain
8	chr4:151069600-151075400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:151070000-151072600	Enhancers	Ovary	ovary
10	chr4:151070400-151072200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr4:151070600-151072200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:151070600-151072600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:151070600-151072600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:151070600-151072600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr4:151070600-151072800	Enhancers	Brain Germinal Matrix	brain
16	chr4:151070800-151072000	Enhancers	HSMMtube	muscle
17	chr4:151070800-151074200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:151070800-151080600	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:151071000-151072600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:151071000-151073600	Weak transcription	A549	lung
21	chr4:151071200-151072200	Weak transcription	Fetal Brain Male	brain
22	chr4:151071400-151072200	Enhancers	Right Atrium	heart
23	chr4:151071400-151091400	Weak transcription	Osteobl	bone
24	chr4:151071600-151072600	Enhancers	Fetal Brain Female	brain
25	chr4:151071600-151072800	Enhancers	Fetal Heart	heart
26	chr4:151071600-151073600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:151071600-151080400	Weak transcription	NHLF	lung
28	chr4:151071600-151091600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:151071800-151072000	Enhancers	Brain Anterior Caudate	brain
30	chr4:151071800-151072200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:151071800-151072200	Enhancers	Right Ventricle	heart
32	chr4:151071800-151072200	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr4:151071800-151072600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:151071800-151072600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:151071800-151072600	Enhancers	Colon Smooth Muscle	Colon
36	chr4:151071800-151072600	Enhancers	Fetal Stomach	stomach
37	chr4:151071800-151072600	Enhancers	Psoas Muscle	Psoas
38	chr4:151071800-151072600	Enhancers	Rectal Smooth Muscle	rectum
39	chr4:151071800-151072600	Enhancers	Stomach Smooth Muscle	stomach
40	chr4:151071800-151073000	Enhancers	Left Ventricle	heart

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