Variant report

Variant	rs2611836
Chromosome Location	chr3:101449733-101449734
allele	A/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	ARID3A	chr3:101449655-101450027	K562	blood:	n/a	n/a
2	CUX1	chr3:101449647-101449965	K562	blood:	n/a	n/a
3	TEAD4	chr3:101449732-101450007	K562	blood:	n/a	n/a
4	ZNF384	chr3:101449591-101450074	K562	blood:	n/a	n/a
5	GATA1	chr3:101449575-101450409	PBDE	blood:	n/a	chr3:101449900-101449907 chr3:101449907-101449924

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101442986..101444875-chr3:101449623..101452459,2	K562	blood:
2	chr3:101442812..101446564-chr3:101447514..101451312,4	MCF-7	breast:

Variant related genes	Relation type
CEP97	TF binding region
ENSG00000182504	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1569071	0.86[TSI][hapmap]
rs2449492	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2449493	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2466369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2611840	1.00[ASN][1000 genomes]
rs2625282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625283	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2625289	0.96[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs2722162	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2722166	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665631	1.00[MEX][hapmap]
rs6764700	1.00[TSI][hapmap];0.91[YRI][hapmap]
rs6788864	0.86[TSI][hapmap]
rs6794860	1.00[ASW][hapmap];1.00[TSI][hapmap]
rs6805496	1.00[TSI][hapmap]
rs6806256	1.00[TSI][hapmap]

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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2611836	FAM55C	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101444600-101450200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:101444600-101450400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:101444600-101450800	Weak transcription	Lung	lung
4	chr3:101444600-101451000	Weak transcription	Gastric	stomach
5	chr3:101444600-101452800	Weak transcription	Spleen	Spleen
6	chr3:101444600-101453200	Weak transcription	Pancreas	Pancrea
7	chr3:101444600-101454800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:101444800-101450000	Weak transcription	Ovary	ovary
9	chr3:101444800-101450200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:101444800-101450400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:101444800-101451000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:101444800-101451000	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:101444800-101451000	Weak transcription	Esophagus	oesophagus
14	chr3:101444800-101451000	Weak transcription	Psoas Muscle	Psoas
15	chr3:101444800-101453400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:101444800-101454200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:101445000-101449800	Weak transcription	HSMMtube	muscle
18	chr3:101445000-101450400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:101445000-101450600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:101445000-101450800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:101445000-101450800	Weak transcription	Aorta	Aorta
22	chr3:101445000-101450800	Weak transcription	Liver	Liver
23	chr3:101445000-101450800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:101445000-101451000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:101445000-101451000	Weak transcription	Colonic Mucosa	Colon
26	chr3:101445000-101451200	Weak transcription	Small Intestine	intestine
27	chr3:101445000-101453000	Weak transcription	Stomach Mucosa	stomach
28	chr3:101445000-101453200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:101445200-101449800	Weak transcription	NHEK	skin
30	chr3:101445200-101450200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:101445200-101450800	Weak transcription	Adipose Nuclei	Adipose
32	chr3:101445200-101450800	Weak transcription	Fetal Kidney	kidney
33	chr3:101445200-101452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:101445200-101453000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:101445400-101450000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:101445400-101453000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:101445400-101455600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:101445400-101455600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:101445600-101450200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:101445600-101450200	Weak transcription	Osteobl	bone
41	chr3:101445600-101452400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:101445600-101454600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr3:101445600-101456400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:101445600-101497400	Weak transcription	Fetal Heart	heart
45	chr3:101445800-101450600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:101445800-101452800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:101445800-101453400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:101445800-101454200	Strong transcription	HSMM	muscle
49	chr3:101445800-101454400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr3:101445800-101454600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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