Variant report

Variant	rs6446740
Chromosome Location	chr4:3409383-3409384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3403449..3406245-chr4:3407590..3409383,2	K562	blood:
2	chr4:3407565..3409961-chr4:3422127..3423905,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10029047	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12644442	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs13109976	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13127597	0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.83[EUR][1000 genomes]
rs13131192	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13152128	0.92[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs1320762	0.80[CHD][hapmap]
rs1320763	0.81[JPT][hapmap]
rs1406674	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1406675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16843157	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs16844307	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs16844309	0.84[CHD][hapmap]
rs1730769	0.94[ASN][1000 genomes]
rs17797467	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs1894442	0.80[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes]
rs1962767	1.00[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3213506	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs4690090	0.86[JPT][hapmap]
rs4690093	0.89[ASN][1000 genomes]
rs6828057	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9790656	0.86[JPT][hapmap]
rs9995777	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv933265	chr4:3392824-4283640	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
11	esv2757918	chr4:3394344-4350986	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer 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 miRNA target site	64 gene(s)	inside rSNPs	diseases
12	esv2759219	chr4:3394344-4350986	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS 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	64 gene(s)	inside rSNPs	diseases
13	nsv461166	chr4:3405165-3451109	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv593450	chr4:3405165-3451109	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv878464	chr4:3405165-3505448	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv878465	chr4:3405165-3566567	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	esv1791851	chr4:3407753-3534022	Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6446740	CRMP1	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3390000-3417200	Weak transcription	Gastric	stomach
2	chr4:3391000-3414000	Weak transcription	Primary T cells from cord blood	blood
3	chr4:3391800-3424200	Weak transcription	Colonic Mucosa	Colon
4	chr4:3392000-3417200	Weak transcription	Pancreas	Pancrea
5	chr4:3392400-3409800	Weak transcription	Spleen	Spleen
6	chr4:3399200-3432200	Weak transcription	Right Atrium	heart
7	chr4:3401600-3416200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:3401800-3416000	Weak transcription	Right Ventricle	heart
9	chr4:3403400-3417200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:3404800-3414200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:3405000-3410800	Strong transcription	Esophagus	oesophagus
12	chr4:3405000-3415000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:3405200-3415800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:3405200-3418800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:3406200-3410000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr4:3406400-3409400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:3406400-3410000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:3406400-3417200	Weak transcription	HMEC	breast
19	chr4:3406600-3410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:3406600-3410400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:3406600-3413800	Weak transcription	Adipose Nuclei	Adipose
22	chr4:3406600-3417200	Weak transcription	HSMM	muscle
23	chr4:3406800-3415600	Weak transcription	Lung	lung
24	chr4:3406800-3417400	Weak transcription	Aorta	Aorta
25	chr4:3407000-3409800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:3407000-3409800	Strong transcription	Fetal Intestine Small	intestine
27	chr4:3407000-3410200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:3407200-3409800	Weak transcription	Fetal Stomach	stomach
29	chr4:3407200-3410600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:3407200-3417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:3407200-3417200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:3407200-3417800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:3407400-3409400	Weak transcription	NHEK	skin
34	chr4:3407400-3410000	Enhancers	Fetal Brain Female	brain
35	chr4:3407400-3415400	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:3407400-3417800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:3407600-3415400	Weak transcription	Fetal Heart	heart
38	chr4:3407600-3417200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:3407600-3418000	Weak transcription	Left Ventricle	heart
40	chr4:3407800-3409600	Enhancers	Liver	Liver
41	chr4:3407800-3409600	Enhancers	HepG2	liver
42	chr4:3407800-3417600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:3408200-3409400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:3408200-3409400	Enhancers	Brain Anterior Caudate	brain
45	chr4:3408200-3409400	Enhancers	Fetal Brain Male	brain
46	chr4:3408200-3414000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:3408200-3416600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr4:3408600-3417200	Weak transcription	HSMMtube	muscle
49	chr4:3408800-3411600	Enhancers	Ovary	ovary
50	chr4:3408800-3436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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