Variant report

Variant	rs446538
Chromosome Location	chr2:40403803-40403804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:40395306..40398028-chr2:40400733..40404513,3	K562	blood:
2	chr2:40401909..40404574-chr3:16441893..16443396,2	MCF-7	breast:
3	chr2:40395306..40398028-chr2:40400733..40404513,4	K562	blood:
4	chr2:40390508..40393940-chr2:40401107..40404487,3	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs105287	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs106706	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12993486	0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.93[ASN][1000 genomes]
rs1428571	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs1651354	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17025367	1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs17025372	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs17025380	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs17025588	0.89[CHB][hapmap]
rs2072529	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2072530	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2270327	0.92[ASN][1000 genomes]
rs2540904	0.89[CHB][hapmap]
rs368577	0.81[CHD][hapmap];0.80[GIH][hapmap];0.83[ASN][1000 genomes]
rs368613	0.84[ASN][1000 genomes]
rs371492	0.87[CHB][hapmap]
rs372072	0.93[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs373273	0.81[ASN][1000 genomes]
rs376303	0.89[CHB][hapmap]
rs376535	0.94[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.80[LWK][hapmap];0.90[ASN][1000 genomes]
rs379804	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs381610	0.88[GIH][hapmap];0.94[MEX][hapmap];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs385341	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs385665	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs388467	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs390145	0.95[CHB][hapmap]
rs392953	0.89[CHB][hapmap]
rs395755	0.81[ASN][1000 genomes]
rs395987	0.89[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs398006	0.84[ASN][1000 genomes]
rs398898	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs402777	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs404005	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs404214	0.89[CHB][hapmap];0.82[MEX][hapmap]
rs404226	0.89[CHB][hapmap]
rs405804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs407148	0.89[CHB][hapmap]
rs408263	0.89[CHB][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs409522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs410912	0.92[ASN][1000 genomes]
rs433572	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[ASN][1000 genomes]
rs447136	0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap]
rs449383	0.84[ASN][1000 genomes]
rs450450	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs473400	0.83[ASN][1000 genomes]
rs481800	0.89[CEU][hapmap]
rs671010	0.83[ASN][1000 genomes]
rs72792740	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs446538	DYNC2LI1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40357800-40406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:40392000-40413200	Weak transcription	Fetal Brain Female	brain
3	chr2:40392600-40405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:40393000-40420000	Weak transcription	Fetal Kidney	kidney
5	chr2:40393600-40416800	Weak transcription	Fetal Stomach	stomach
6	chr2:40394200-40406800	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:40396400-40405400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:40397000-40405000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:40397600-40404800	Weak transcription	Right Ventricle	heart
10	chr2:40397800-40404800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:40398200-40404800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:40398400-40406200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:40399200-40404800	Weak transcription	Left Ventricle	heart
14	chr2:40399400-40404800	Weak transcription	Dnd41	blood
15	chr2:40400000-40404600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:40400600-40426800	Weak transcription	Osteobl	bone
17	chr2:40400800-40404600	Weak transcription	NHDF-Ad	bronchial
18	chr2:40401000-40404600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:40401000-40405400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:40401200-40404600	Weak transcription	HSMM	muscle
21	chr2:40401800-40404600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:40402200-40407400	Enhancers	Fetal Heart	heart
23	chr2:40403200-40405200	Weak transcription	HSMMtube	muscle

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