Variant report

Variant	rs10496035
Chromosome Location	chr2:55177305-55177306
allele	C/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	RCOR1	chr2:55176306-55177695	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55176432..55179496-chr2:55180651..55183314,3	MCF-7	breast:

Variant related genes	Relation type
EML6	TF binding region
ENSG00000214595	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10460507	0.83[LWK][hapmap];0.84[AFR][1000 genomes]
rs11898145	0.84[AFR][1000 genomes]
rs12619758	1.00[CEU][hapmap];0.98[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17346629	0.84[MKK][hapmap]
rs6741304	0.84[MKK][hapmap]
rs7565735	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7569471	0.86[LWK][hapmap]
rs7592371	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[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	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
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10496035	CCDC104	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55168800-55193400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55170400-55190400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:55173000-55193400	Weak transcription	Aorta	Aorta
4	chr2:55173200-55179800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:55173200-55187000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:55173200-55203400	Weak transcription	Gastric	stomach
7	chr2:55173400-55184600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:55173600-55181200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:55173600-55194000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:55173600-55195000	Weak transcription	Pancreas	Pancrea
11	chr2:55173800-55178600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:55173800-55178800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:55173800-55180000	Weak transcription	HSMMtube	muscle
14	chr2:55174000-55178800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:55174000-55178800	Weak transcription	HSMM	muscle
16	chr2:55174800-55194000	Weak transcription	Brain Germinal Matrix	brain
17	chr2:55175000-55177800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:55175200-55178800	Weak transcription	Osteobl	bone
19	chr2:55175400-55193200	Weak transcription	Fetal Brain Female	brain
20	chr2:55175600-55177800	Weak transcription	Adipose Nuclei	Adipose
21	chr2:55175600-55178000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:55175600-55185600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:55175600-55185800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:55175600-55185800	Weak transcription	Brain Substantia Nigra	brain
25	chr2:55175600-55194600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:55175800-55177800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:55175800-55181600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:55175800-55184600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:55175800-55193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:55176000-55182400	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:55176000-55182800	Weak transcription	Fetal Intestine Small	intestine
32	chr2:55176200-55177600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:55176200-55180600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:55176400-55184600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:55176600-55179200	Enhancers	K562	blood
36	chr2:55176600-55180800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:55177200-55178400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:55177200-55178800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:55177200-55178800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:55177200-55178800	Weak transcription	NHDF-Ad	bronchial
41	chr2:55177200-55179000	Weak transcription	NHLF	lung

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