Variant report

Variant	rs1949882
Chromosome Location	chr3:133602133-133602134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133599032..133602224-chr3:133604113..133606875,3	MCF-7	breast:
2	chr3:133600203..133603946-chr3:133604240..133607293,3	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1106735	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs1917778	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917779	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs1949881	0.93[YRI][hapmap]
rs2140921	0.86[ASN][1000 genomes]
rs2370638	0.86[ASN][1000 genomes]
rs2692682	0.88[CHB][hapmap];0.93[CHD][hapmap]
rs2692686	0.86[ASN][1000 genomes]
rs2715616	0.86[ASN][1000 genomes]
rs2715620	0.88[CHB][hapmap]
rs2715630	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap]
rs2715635	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7610245	0.86[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	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1949882	CEP70	cis	parietal	SCAN
rs1949882	ARMC8	cis	parietal	SCAN
rs1949882	CCRL1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133590600-133606600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:133592400-133602800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:133592400-133605800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:133596400-133613600	Weak transcription	Gastric	stomach
5	chr3:133598600-133602800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:133598800-133610400	Weak transcription	Fetal Brain Male	brain
7	chr3:133599000-133602200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:133599000-133602200	Enhancers	GM12878-XiMat	blood
9	chr3:133599400-133602600	Weak transcription	Left Ventricle	heart
10	chr3:133599400-133602800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:133599600-133610600	Weak transcription	Pancreas	Pancrea
12	chr3:133599800-133603000	Weak transcription	Spleen	Spleen
13	chr3:133599800-133606200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:133600000-133602200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:133600000-133603600	Enhancers	K562	blood
16	chr3:133600200-133603600	Enhancers	Stomach Mucosa	stomach
17	chr3:133600400-133602800	Enhancers	Placenta	Placenta
18	chr3:133600800-133602200	ZNF genes & repeats	Fetal Brain Female	brain
19	chr3:133600800-133602400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:133601000-133608200	Enhancers	Brain Anterior Caudate	brain
21	chr3:133601200-133602200	Weak transcription	Right Atrium	heart
22	chr3:133601200-133603600	Enhancers	Brain Substantia Nigra	brain
23	chr3:133601200-133612800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:133601400-133602200	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:133601400-133602400	Strong transcription	Brain Germinal Matrix	brain
26	chr3:133601400-133602800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr3:133601400-133603000	Enhancers	Colonic Mucosa	Colon
28	chr3:133601400-133604400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:133601400-133612800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:133601600-133602400	Enhancers	Brain Hippocampus Middle	brain
31	chr3:133601600-133602400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:133601600-133602800	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr3:133601600-133603000	Enhancers	Right Ventricle	heart
34	chr3:133601800-133607000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:133602000-133602200	Enhancers	Brain Angular Gyrus	brain
36	chr3:133602000-133602800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr3:133602000-133603400	Enhancers	Adipose Nuclei	Adipose
38	chr3:133602000-133603400	Enhancers	Duodenum Mucosa	Duodenum
39	chr3:133602000-133603400	Enhancers	Ovary	ovary

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