Variant report

Variant	rs17046477
Chromosome Location	chr2:55129148-55129149
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	chr2:55092274..55094701-chr2:55126446..55129153,2	K562	blood:
2	chr2:55127373..55130135-chr2:55130954..55133199,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10171653	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12464877	1.00[ASW][hapmap]
rs12467381	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17046514	1.00[ASW][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap]
rs2304687	0.81[ASN][1000 genomes]
rs2580768	1.00[ASW][hapmap]
rs2580770	1.00[ASW][hapmap]
rs2580771	1.00[ASW][hapmap]
rs2588515	1.00[ASW][hapmap]
rs34121514	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36126551	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4671987	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671988	0.92[EUR][1000 genomes]
rs4671989	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671993	1.00[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs4672003	1.00[ASW][hapmap]
rs60808665	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6707572	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67299431	0.88[EUR][1000 genomes]
rs6734314	1.00[ASW][hapmap]
rs919669	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17046477	CCDC104	cis	parietal	SCAN
rs17046477	CCDC88A	cis	cerebellum	SCAN
rs17046477	ERLEC1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55095200-55148200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55120400-55130200	Weak transcription	Hela-S3	cervix
3	chr2:55122000-55130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:55123400-55130800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:55125800-55131000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:55126000-55130800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:55126000-55131000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:55126000-55131200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:55126200-55130800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:55126600-55129200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:55126600-55129800	Enhancers	Fetal Intestine Large	intestine
12	chr2:55127000-55130600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:55127000-55132400	Weak transcription	Fetal Brain Male	brain
14	chr2:55127400-55129200	Enhancers	Liver	Liver
15	chr2:55127400-55129600	Enhancers	Fetal Intestine Small	intestine
16	chr2:55127600-55130400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:55127600-55130600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:55127600-55130600	Weak transcription	HSMMtube	muscle
19	chr2:55127600-55131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:55127600-55131400	Weak transcription	Fetal Thymus	thymus
21	chr2:55127600-55133400	Weak transcription	Fetal Brain Female	brain
22	chr2:55127800-55129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:55127800-55130400	Weak transcription	Osteobl	bone
24	chr2:55127800-55133400	Weak transcription	Brain Substantia Nigra	brain
25	chr2:55127800-55133600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:55128000-55130000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:55128000-55130000	Weak transcription	NHEK	skin
28	chr2:55128000-55130800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:55128000-55131000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:55128000-55133400	Weak transcription	Brain Angular Gyrus	brain
31	chr2:55128000-55133400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:55128000-55133800	Weak transcription	Brain Anterior Caudate	brain
33	chr2:55128200-55129200	Enhancers	Fetal Muscle Leg	muscle
34	chr2:55128400-55130800	Weak transcription	Small Intestine	intestine
35	chr2:55128800-55129200	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr2:55128800-55129200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr2:55128800-55129200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr2:55128800-55129400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:55128800-55129400	Enhancers	NHDF-Ad	bronchial
40	chr2:55129000-55129200	Enhancers	Adipose Nuclei	Adipose
41	chr2:55129000-55129200	Enhancers	Brain Hippocampus Middle	brain
42	chr2:55129000-55129800	Enhancers	Psoas Muscle	Psoas
43	chr2:55129000-55131600	Weak transcription	HepG2	liver

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