Variant report

Variant	rs17701871
Chromosome Location	chr12:4777349-4777350
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:36)

rs_ID	r²[population]
rs11063307	1.00[ASN][1000 genomes]
rs12809178	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs12816272	1.00[ASN][1000 genomes]
rs12817218	1.00[ASN][1000 genomes]
rs12821116	1.00[ASN][1000 genomes]
rs12827952	1.00[ASN][1000 genomes]
rs12831221	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs16931649	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286579	1.00[ASN][1000 genomes]
rs34205979	1.00[ASN][1000 genomes]
rs34214125	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34337517	1.00[ASN][1000 genomes]
rs34475613	1.00[ASN][1000 genomes]
rs34502100	1.00[ASN][1000 genomes]
rs34765166	1.00[ASN][1000 genomes]
rs34947765	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34952740	1.00[ASN][1000 genomes]
rs35016874	1.00[ASN][1000 genomes]
rs35288424	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35464779	1.00[ASN][1000 genomes]
rs35562639	1.00[ASN][1000 genomes]
rs35878255	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35899818	1.00[ASN][1000 genomes]
rs35925396	1.00[ASN][1000 genomes]
rs4766273	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5007510	1.00[ASN][1000 genomes]
rs55760751	1.00[ASN][1000 genomes]
rs59096706	1.00[ASN][1000 genomes]
rs59986414	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66703365	1.00[ASN][1000 genomes]
rs67871557	1.00[ASN][1000 genomes]
rs68144469	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71459918	1.00[ASN][1000 genomes]
rs73038876	1.00[ASN][1000 genomes]
rs7306593	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960763	1.00[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	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1036308	chr12:4748657-4804156	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17701871	CLEC4A	cis	cerebellum	SCAN
rs17701871	AKAP3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4759000-4799400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:4760800-4782400	Strong transcription	Primary T cells from cord blood	blood
3	chr12:4761800-4782200	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:4762200-4779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:4762200-4783600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:4762600-4779600	Strong transcription	Primary hematopoietic stem cells	blood
7	chr12:4762600-4780000	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:4762600-4782800	Strong transcription	Adipose Nuclei	Adipose
9	chr12:4762800-4779800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:4762800-4781000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:4762800-4782000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:4763000-4780400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:4763000-4782200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:4763000-4782400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:4763000-4782400	Strong transcription	Placenta	Placenta
16	chr12:4763000-4783000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr12:4763200-4782200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:4763400-4779200	Strong transcription	Brain Germinal Matrix	brain
19	chr12:4763400-4779600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:4763400-4779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:4763400-4780400	Strong transcription	Fetal Thymus	thymus
22	chr12:4763400-4781200	Strong transcription	GM12878-XiMat	blood
23	chr12:4763400-4781200	Strong transcription	NH-A	brain
24	chr12:4763400-4781400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:4763400-4781600	Strong transcription	Brain Anterior Caudate	brain
26	chr12:4763400-4781600	Strong transcription	Dnd41	blood
27	chr12:4763400-4782000	Strong transcription	Fetal Kidney	kidney
28	chr12:4763400-4782200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:4763400-4782200	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr12:4763400-4782200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:4763400-4782200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr12:4763400-4782400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:4763400-4782400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:4763400-4782400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:4763400-4782600	Strong transcription	Liver	Liver
36	chr12:4763400-4782600	Strong transcription	Fetal Intestine Large	intestine
37	chr12:4763400-4782800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:4763400-4782800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr12:4763400-4782800	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:4763400-4783000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:4763400-4783000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:4763400-4783000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:4763400-4783000	Strong transcription	Fetal Lung	lung
44	chr12:4763400-4783000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr12:4763600-4779800	Strong transcription	Fetal Brain Female	brain
46	chr12:4763600-4780600	Strong transcription	Primary B cells from cord blood	blood
47	chr12:4763600-4782400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr12:4763600-4782400	Strong transcription	Left Ventricle	heart
49	chr12:4764000-4780000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:4766400-4782400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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