Variant report

Variant	rs16907810
Chromosome Location	chr12:12327655-12327656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10431232	0.86[EUR][1000 genomes]
rs10431303	0.85[EUR][1000 genomes]
rs10743981	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1074992	0.87[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs1074993	0.85[EUR][1000 genomes]
rs10772544	0.83[EUR][1000 genomes]
rs10845498	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10845504	0.87[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs11054697	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11054701	0.92[ASW][hapmap];0.94[CEU][hapmap];0.88[GIH][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11054752	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1181333	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1468878	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1548958	0.85[EUR][1000 genomes]
rs16907786	0.84[ASW][hapmap];0.94[CEU][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2075241	0.92[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2160521	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2160589	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2300231	0.92[ASW][hapmap];0.94[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2417090	0.83[EUR][1000 genomes]
rs3825258	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4265667	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4494380	0.83[EUR][1000 genomes]
rs4619236	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs4763789	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61130413	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7134001	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7136380	0.80[EUR][1000 genomes]
rs7295656	0.85[EUR][1000 genomes]
rs7310538	0.84[EUR][1000 genomes]
rs7311987	0.83[EUR][1000 genomes]
rs7313285	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7968660	0.87[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS 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 lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16907810	DERA	cis	parietal	SCAN
rs16907810	M6PR	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
4	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
6	chr12:12288200-12342800	Weak transcription	K562	blood
7	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:12303800-12335600	Weak transcription	Right Ventricle	heart
9	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:12312000-12332600	Weak transcription	Dnd41	blood
11	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:12312200-12334000	Weak transcription	Pancreas	Pancrea
13	chr12:12312200-12334600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:12312200-12338000	Weak transcription	Brain Germinal Matrix	brain
15	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
17	chr12:12312400-12332400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:12312400-12332600	Weak transcription	Fetal Thymus	thymus
19	chr12:12312800-12337600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:12314000-12331400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:12314000-12333200	Weak transcription	NH-A	brain
22	chr12:12314000-12335600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:12314000-12336000	Weak transcription	Adipose Nuclei	Adipose
24	chr12:12314200-12328000	Weak transcription	Ovary	ovary
25	chr12:12314400-12336000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:12315400-12334000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:12315400-12340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:12315400-12371600	Weak transcription	Lung	lung
29	chr12:12316200-12332400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:12317400-12332400	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:12317600-12330800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:12317600-12331400	Weak transcription	HUVEC	blood vessel
33	chr12:12317600-12331600	Weak transcription	Fetal Intestine Large	intestine
34	chr12:12317600-12332800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr12:12317600-12335600	Weak transcription	Fetal Stomach	stomach
36	chr12:12317800-12330200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:12317800-12330600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:12317800-12335400	Weak transcription	Fetal Kidney	kidney
39	chr12:12318000-12330400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:12318200-12330400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:12318200-12330400	Weak transcription	Fetal Brain Male	brain
42	chr12:12318200-12330800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:12318200-12331400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:12318200-12335600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:12318200-12335600	Weak transcription	Left Ventricle	heart
46	chr12:12318200-12335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:12318400-12334000	Weak transcription	Brain Substantia Nigra	brain
48	chr12:12321400-12330200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:12322000-12329000	Weak transcription	Liver	Liver
50	chr12:12322000-12334200	Weak transcription	Gastric	stomach

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