Variant report

Variant	rs10171653
Chromosome Location	chr2:55127601-55127602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55092274..55094701-chr2:55126446..55129153,2	K562	blood:
2	chr2:55126912..55127637-chr2:55402459..55403324,2	K562	blood:
3	chr2:55126891..55127632-chr2:55402484..55403169,4	MCF-7	breast:
4	chr2:55127373..55130135-chr2:55130954..55133199,2	K562	blood:
5	chr2:55126697..55127637-chr2:55395567..55396788,4	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10201734	0.88[ASN][1000 genomes]
rs12467381	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17046477	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34121514	0.81[EUR][1000 genomes]
rs36126551	0.83[EUR][1000 genomes]
rs4671987	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4671988	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671989	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671990	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671991	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60808665	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6545456	0.88[ASN][1000 genomes]
rs6707572	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7355716	0.83[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs919669	0.83[AMR][1000 genomes];0.84[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10171653	CCDC88A	cis	cerebellum	SCAN
rs10171653	CCDC104	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	chr2:55123200-55128200	Weak transcription	HepG2	liver
5	chr2:55123400-55130800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:55125400-55128800	Enhancers	Duodenum Mucosa	Duodenum
7	chr2:55125800-55131000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:55126000-55130800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:55126000-55131000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:55126000-55131200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:55126200-55130800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:55126400-55128000	Enhancers	Fetal Muscle Leg	muscle
13	chr2:55126600-55127800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:55126600-55128600	Enhancers	Brain Hippocampus Middle	brain
15	chr2:55126600-55129200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:55126600-55129800	Enhancers	Fetal Intestine Large	intestine
17	chr2:55126800-55127800	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:55126800-55127800	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr2:55126800-55127800	Enhancers	Brain Substantia Nigra	brain
20	chr2:55126800-55127800	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr2:55126800-55128000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:55126800-55128000	Enhancers	Brain Angular Gyrus	brain
23	chr2:55127000-55128000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:55127000-55130600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:55127000-55132400	Weak transcription	Fetal Brain Male	brain
26	chr2:55127200-55128000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr2:55127400-55127800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:55127400-55128000	Enhancers	Brain Anterior Caudate	brain
29	chr2:55127400-55128000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:55127400-55128000	Enhancers	NHEK	skin
31	chr2:55127400-55129200	Enhancers	Liver	Liver
32	chr2:55127400-55129600	Enhancers	Fetal Intestine Small	intestine
33	chr2:55127600-55127800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:55127600-55128000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:55127600-55128200	Weak transcription	Small Intestine	intestine
36	chr2:55127600-55128800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:55127600-55128800	Weak transcription	NHDF-Ad	bronchial
38	chr2:55127600-55130400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:55127600-55130600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:55127600-55130600	Weak transcription	HSMMtube	muscle
41	chr2:55127600-55131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:55127600-55131400	Weak transcription	Fetal Thymus	thymus
43	chr2:55127600-55133400	Weak transcription	Fetal Brain Female	brain

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