Variant report

Variant	rs7957057
Chromosome Location	chr12:40690706-40690707
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10467144	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs10467146	0.87[CEU][hapmap]
rs10735931	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10748029	0.85[ASN][1000 genomes]
rs10748030	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10748033	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10748034	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784486	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784501	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784503	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784504	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784506	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784509	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784528	0.83[YRI][hapmap]
rs10784548	0.87[CEU][hapmap]
rs10784585	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs10878290	0.86[ASN][1000 genomes]
rs10878358	0.85[ASN][1000 genomes]
rs10878368	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs10878371	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs10878377	0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10878441	0.83[CEU][hapmap]
rs11176013	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs12314982	0.87[CEU][hapmap]
rs12426362	0.87[CEU][hapmap]
rs1427263	0.86[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1427264	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs1427265	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs1427266	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs1427267	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17466605	0.87[CEU][hapmap]
rs1896252	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs1896253	0.87[CHB][hapmap]
rs1896254	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs2069228	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2081700	0.91[CEU][hapmap]
rs2081701	0.91[CEU][hapmap]
rs2114568	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs2114569	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs2162469	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs2896975	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2896982	0.87[CEU][hapmap]
rs3761863	0.87[CEU][hapmap]
rs3886747	0.87[CEU][hapmap]
rs4280068	0.87[CEU][hapmap]
rs4310676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473003	0.86[ASW][hapmap];0.83[YRI][hapmap]
rs4483664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767969	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs4767973	0.87[CEU][hapmap]
rs4768224	0.93[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768227	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs4768229	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs4768236	0.87[CEU][hapmap]
rs4768237	0.87[CEU][hapmap]
rs7134408	0.87[CEU][hapmap]
rs7137160	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs7137665	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs715402	0.83[YRI][hapmap]
rs721709	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs721711	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs721712	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs721713	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs7298930	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs7302503	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7305344	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7307276	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs7307310	0.86[ASW][hapmap];0.83[YRI][hapmap]
rs7307562	0.84[CHD][hapmap]
rs7308193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310390	0.87[CEU][hapmap]
rs7488873	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954300	0.87[CEU][hapmap]
rs7954318	0.87[CEU][hapmap]
rs7963086	0.83[YRI][hapmap]
rs7973479	0.82[CHB][hapmap]
rs7975124	0.86[CEU][hapmap]
rs7979341	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs963243	0.91[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1042967	chr12:40629636-40710319	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7957057	KIF21A	cis	parietal	SCAN
rs7957057	LRRK2	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
2	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
3	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
4	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
5	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:40659600-40694600	Weak transcription	Psoas Muscle	Psoas
7	chr12:40659600-40711200	Weak transcription	Aorta	Aorta
8	chr12:40661600-40696400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:40673400-40713400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:40674400-40760400	Weak transcription	Lung	lung
11	chr12:40677000-40712200	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:40679000-40696200	Weak transcription	Right Ventricle	heart
13	chr12:40679200-40699400	Weak transcription	Fetal Kidney	kidney
14	chr12:40680400-40692600	Weak transcription	Small Intestine	intestine
15	chr12:40680400-40709000	Weak transcription	Ovary	ovary
16	chr12:40681000-40694200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:40682000-40694400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:40684000-40697800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:40684000-40722600	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:40684000-40722600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:40684000-40725000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:40687400-40691000	Strong transcription	Primary B cells from cord blood	blood
25	chr12:40688800-40691400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:40689000-40692000	Strong transcription	Liver	Liver
27	chr12:40689000-40692400	Strong transcription	Adipose Nuclei	Adipose
28	chr12:40689800-40694600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:40690400-40709200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:40690600-40691000	Strong transcription	A549	lung

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