Variant report

Variant	rs2641558
Chromosome Location	chr12:63178779-63178780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62995008..63000778-chr12:63178750..63184772,7	MCF-7	breast:
2	chr12:62995127..63000683-chr12:63174450..63183073,15	MCF-7	breast:
3	chr12:63174127..63177052-chr12:63177442..63179334,2	K562	blood:

Variant related genes	Relation type
ENSG00000257354	Chromatin interaction
ENSG00000199179	Chromatin interaction
ENSG00000221949	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs337515	0.94[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899160	chr12:63149213-63209623	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2641558	AGAP2	cis	cerebellum	SCAN
rs2641558	B4GALNT1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63150000-63179800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:63161400-63180000	Weak transcription	Aorta	Aorta
3	chr12:63161800-63179400	Weak transcription	Brain Angular Gyrus	brain
4	chr12:63165600-63182000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:63166600-63179600	Weak transcription	NHLF	lung
6	chr12:63168200-63180000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:63171400-63180000	Weak transcription	Colonic Mucosa	Colon
8	chr12:63171400-63180000	Weak transcription	Fetal Intestine Large	intestine
9	chr12:63174800-63182800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:63175000-63179800	Weak transcription	Spleen	Spleen
11	chr12:63175200-63193600	Weak transcription	Gastric	stomach
12	chr12:63175200-63206800	Weak transcription	Pancreas	Pancrea
13	chr12:63175400-63179400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:63175400-63180000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:63175600-63179400	Weak transcription	Fetal Thymus	thymus
16	chr12:63175600-63179600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:63175600-63179600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:63175600-63180000	Weak transcription	Fetal Intestine Small	intestine
19	chr12:63176600-63180200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:63176800-63179600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:63177000-63178800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:63177000-63178800	Enhancers	Osteobl	bone
23	chr12:63177000-63182600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:63177200-63178800	Enhancers	Brain Hippocampus Middle	brain
25	chr12:63177400-63179400	Enhancers	HUVEC	blood vessel
26	chr12:63177400-63181600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:63177600-63178800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr12:63177600-63178800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:63177600-63179600	Weak transcription	HSMMtube	muscle
30	chr12:63177800-63178800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:63177800-63179200	Enhancers	A549	lung
32	chr12:63177800-63179400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:63177800-63179800	Enhancers	HMEC	breast
34	chr12:63177800-63180600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:63177800-63181800	Enhancers	NH-A	brain
36	chr12:63178000-63179400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:63178000-63179400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:63178000-63179400	Enhancers	Hela-S3	cervix
39	chr12:63178000-63179800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:63178000-63180000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr12:63178000-63185400	Weak transcription	Fetal Brain Male	brain
42	chr12:63178200-63179400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:63178200-63179400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:63178200-63179400	Weak transcription	Fetal Muscle Leg	muscle
45	chr12:63178200-63179600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:63178200-63179600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:63178200-63179800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:63178200-63179800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:63178200-63179800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:63178200-63179800	Weak transcription	Brain Inferior Temporal Lobe	brain

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