Variant report

Variant	rs2896975
Chromosome Location	chr12:40706375-40706376
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:40706340-40707378	SK-N-SH	brain:	n/a	chr12:40706972-40706991
2	CTCF	chr12:40706286-40707415	A549	lung:	n/a	chr12:40706975-40706991 chr12:40706974-40706992 chr12:40706977-40706987 chr12:40706969-40706990
3	NRF1	chr12:40706322-40706470	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRRK2	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10467144	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10735931	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10748029	0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10748030	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10748033	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10748034	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784486	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784501	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784503	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784504	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784506	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784509	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784528	0.94[YRI][hapmap]
rs10784585	0.87[CEU][hapmap]
rs10878358	0.87[ASN][1000 genomes]
rs10878368	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10878371	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10878377	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10878441	0.82[CHB][hapmap]
rs11176013	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12314982	0.80[CEU][hapmap]
rs12426362	0.81[CEU][hapmap]
rs1427263	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1427264	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1427265	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1427266	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1427267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17466605	0.81[CEU][hapmap]
rs1896252	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1896253	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1896254	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2069228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2081700	0.84[CEU][hapmap]
rs2081701	0.84[CEU][hapmap]
rs2114568	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2114569	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2162469	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2896982	0.80[CEU][hapmap]
rs4280068	0.80[CEU][hapmap]
rs4310676	0.92[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4473003	0.94[YRI][hapmap]
rs4483664	0.92[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767969	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs4767973	0.81[CEU][hapmap]
rs4768224	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4768227	0.86[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs4768229	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs4768237	0.81[CEU][hapmap]
rs7134408	0.81[CEU][hapmap]
rs7137160	0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7137665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs715402	0.94[YRI][hapmap]
rs721709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721711	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs721712	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs721713	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7298930	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7302503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7305344	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7307276	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7307310	0.94[YRI][hapmap]
rs7307562	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs7308193	0.92[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310390	0.80[CEU][hapmap]
rs7488873	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954300	0.80[CEU][hapmap]
rs7954318	0.80[CEU][hapmap]
rs7957057	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]
rs7963086	0.94[YRI][hapmap]
rs7979341	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs963243	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
2	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
3	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
4	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr12:40659600-40711200	Weak transcription	Aorta	Aorta
6	chr12:40673400-40713400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:40674400-40760400	Weak transcription	Lung	lung
8	chr12:40677000-40712200	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:40680400-40709000	Weak transcription	Ovary	ovary
10	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:40684000-40722600	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:40684000-40722600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:40684000-40725000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:40690400-40709200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:40692400-40711600	Weak transcription	Adipose Nuclei	Adipose
17	chr12:40695800-40723600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:40699600-40721800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:40702400-40706800	Strong transcription	Primary B cells from cord blood	blood
20	chr12:40704200-40706800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:40704400-40709000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:40704400-40723800	Weak transcription	Brain Anterior Caudate	brain
23	chr12:40704600-40706400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:40704600-40708000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:40704800-40709000	Weak transcription	Liver	Liver
26	chr12:40705200-40706800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:40705600-40722400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:40705800-40706800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:40705800-40707000	Enhancers	A549	lung
30	chr12:40706000-40706600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr12:40706000-40706800	Enhancers	HMEC	breast
32	chr12:40706200-40706800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:40706200-40706800	Enhancers	NHEK	skin

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