Variant report

Variant	rs235868
Chromosome Location	chr1:171610740-171610741
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	chr1:171610292..171610843-chr1:171953542..171954408,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs171001	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs171002	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs182907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs183532	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2032555	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235861	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235869	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs235870	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs235871	0.94[ASN][1000 genomes]
rs235873	0.94[ASN][1000 genomes]
rs235874	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235876	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs235877	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235878	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs235881	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235882	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs483849	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs603490	0.91[ASN][1000 genomes]
rs603930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs604864	0.92[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6425364	1.00[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs86857	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv999578	chr1:171578076-171610740	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv528322	chr1:171578532-171612267	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv548191	chr1:171578532-171612267	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs235868	DNM3	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171605600-171610800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:171605800-171614400	Weak transcription	Aorta	Aorta
3	chr1:171607800-171612400	Weak transcription	Adipose Nuclei	Adipose
4	chr1:171607800-171614000	Weak transcription	HepG2	liver
5	chr1:171609400-171610800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr1:171609400-171611200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr1:171609600-171611000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:171609600-171612400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:171609800-171610800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:171609800-171611600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:171610000-171610800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:171610000-171611200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr1:171610000-171611400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:171610000-171611400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:171610000-171614000	Weak transcription	Spleen	Spleen
16	chr1:171610200-171610800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:171610200-171610800	Enhancers	Ovary	ovary
18	chr1:171610400-171610800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:171610400-171611600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:171610600-171610800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr1:171610600-171611000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr1:171610600-171611000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:171610600-171611400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:171610600-171611400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:171610600-171611600	Enhancers	Liver	Liver

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