Variant report

Variant	rs3813229
Chromosome Location	chr2:74056564-74056565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74055755..74057848-chr2:74210321..74213795,3	MCF-7	breast:
2	chr2:74055980..74060254-chr2:74070607..74073353,3	MCF-7	breast:
3	chr2:74055452..74058450-chr2:74210942..74214913,3	K562	blood:
4	chr2:74003041..74008140-chr2:74055591..74058388,4	MCF-7	breast:
5	chr12:92539292..92540065-chr2:74055879..74056721,4	Hela-S3	cervix:
6	chr2:74056477..74058095-chr2:74392122..74393628,2	MCF-7	breast:
7	chr2:74055799..74057566-chr2:74228295..74229864,2	MCF-7	breast:
8	chr2:74055378..74057466-chr2:74084909..74087959,3	K562	blood:
9	chr2:74054992..74057413-chr2:74347412..74349314,2	K562	blood:
10	chr2:73962060..73965748-chr2:74053469..74057980,4	K562	blood:
11	chr2:74056362..74058489-chr2:74217644..74219236,2	K562	blood:
12	chr2:74055188..74061210-chr2:74210942..74215230,5	K562	blood:
13	chr2:74055762..74057828-chr2:74374741..74376324,2	K562	blood:
14	chr2:74054362..74057947-chr2:74372650..74375089,3	MCF-7	breast:
15	chr2:74004444..74007409-chr2:74053786..74057952,3	K562	blood:
16	chr2:74054272..74058005-chr2:74424584..74427795,4	K562	blood:
17	chr2:74055393..74058315-chr2:74373246..74376437,5	K562	blood:
18	chr2:74052797..74060455-chr2:74207744..74214705,21	MCF-7	breast:
19	chr1:28907935..28908482-chr2:74055972..74056830,2	Hela-S3	cervix:
20	chr2:74054349..74056665-chr2:74153840..74155868,2	K562	blood:
21	chr2:74054453..74058790-chr2:74226313..74230079,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000144034	Chromatin interaction
ENSG00000257800	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000124356	Chromatin interaction
ENSG00000245904	Chromatin interaction
ENSG00000114956	Chromatin interaction
ENSG00000197989	Chromatin interaction
ENSG00000144048	Chromatin interaction
ENSG00000237883	Chromatin interaction
ENSG00000255989	Chromatin interaction
ENSG00000133639	Chromatin interaction
ENSG00000163170	Chromatin interaction
ENSG00000187605	Chromatin interaction
ENSG00000235499	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1036113	0.86[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1474335	0.86[CEU][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs17009428	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs33990056	0.82[EUR][1000 genomes]
rs3738846	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs4852983	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6546875	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6722659	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6726010	0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs6737597	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs7566009	0.80[ASN][1000 genomes]
rs7594485	0.86[ASW][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv2780	chr2:73994168-74057248	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3813229	ALMS1P	cis	parietal	SCAN
rs3813229	ALMS1	cis	cerebellum	SCAN
rs3813229	STAMBP	cis	normal skin	skin_eQTL
rs3813229	STAMBP	cis	uninvolved skin	skin_eQTL
rs3813229	ALMS1P	cis	cerebellum	SCAN
rs3813229	ALMS1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74055200-74056800	Active TSS	Hela-S3	cervix
2	chr2:74055200-74057000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:74055200-74057000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr2:74055200-74057000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr2:74055200-74057000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:74055200-74057000	Active TSS	K562	blood
7	chr2:74055200-74057200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:74055200-74058000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:74055400-74056600	Active TSS	Brain Cingulate Gyrus	brain
10	chr2:74055400-74056600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:74055400-74056800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr2:74055400-74057000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr2:74055400-74057000	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr2:74055400-74057000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr2:74055400-74057000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:74055400-74057000	Active TSS	Left Ventricle	heart
17	chr2:74055400-74057200	Active TSS	NHDF-Ad	bronchial
18	chr2:74055400-74057200	Active TSS	NHLF	lung
19	chr2:74055400-74057400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr2:74055400-74057800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:74055600-74056600	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr2:74055600-74056600	Active TSS	Brain Germinal Matrix	brain
23	chr2:74055600-74056600	Active TSS	Colonic Mucosa	Colon
24	chr2:74055600-74056600	Active TSS	Fetal Brain Male	brain
25	chr2:74055600-74056600	Active TSS	Fetal Lung	lung
26	chr2:74055600-74056600	Active TSS	Fetal Muscle Leg	muscle
27	chr2:74055600-74056600	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr2:74055600-74056600	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr2:74055600-74056800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr2:74055600-74056800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:74055600-74056800	Active TSS	Aorta	Aorta
32	chr2:74055600-74056800	Active TSS	Brain Hippocampus Middle	brain
33	chr2:74055600-74056800	Active TSS	Brain Substantia Nigra	brain
34	chr2:74055600-74056800	Active TSS	Fetal Brain Female	brain
35	chr2:74055600-74056800	Active TSS	Fetal Intestine Large	intestine
36	chr2:74055600-74056800	Active TSS	HSMM	muscle
37	chr2:74055600-74057000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:74055600-74057000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:74055600-74057000	Active TSS	Brain Angular Gyrus	brain
40	chr2:74055600-74057000	Active TSS	Placenta	Placenta
41	chr2:74055600-74057000	Active TSS	Ovary	ovary
42	chr2:74055600-74057000	Active TSS	Right Atrium	heart
43	chr2:74055600-74057000	Active TSS	Right Ventricle	heart
44	chr2:74055600-74057000	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr2:74055600-74057000	Active TSS	A549	lung
46	chr2:74055600-74057000	Active TSS	HMEC	breast
47	chr2:74055600-74057200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:74055600-74057200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:74055600-74057200	Active TSS	Fetal Muscle Trunk	muscle
50	chr2:74055600-74057400	Active TSS	HUES64 Cell Line	embryonic stem cell

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