Variant report

Variant	rs330787
Chromosome Location	chr2:48041377-48041378
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	POLR2A	chr2:48040869-48041491	K562	blood:	n/a	n/a
2	POLR2A	chr2:48040847-48041493	U87	brain:	n/a	n/a
3	POLR2A	chr2:48041083-48041385	A549	lung:	n/a	n/a
4	POLR2A	chr2:48040799-48041548	SK-N-MC	brain:	n/a	n/a
5	BCL3	chr2:48040805-48041647	A549	lung:	n/a	n/a
6	POLR2A	chr2:48040829-48041784	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
FBXO11	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12620679	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2020911	0.81[YRI][hapmap]
rs2651766	0.80[ASW][hapmap];0.81[YRI][hapmap]
rs2710163	0.80[ASW][hapmap]
rs56101865	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[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	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats 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
4	nsv930955	chr2:48040218-48121218	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs330787	SLC3A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:48016200-48050400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:48017000-48049400	Strong transcription	Fetal Intestine Large	intestine
4	chr2:48017200-48053200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:48017400-48049600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:48021200-48051600	Strong transcription	Placenta	Placenta
7	chr2:48021400-48067600	Strong transcription	Dnd41	blood
8	chr2:48021600-48067000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:48022000-48041400	Strong transcription	HSMM	muscle
10	chr2:48022200-48050200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr2:48022800-48049200	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr2:48022800-48050000	Strong transcription	HUVEC	blood vessel
13	chr2:48023200-48065000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:48030200-48067600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:48030400-48044200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:48030400-48067000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:48030800-48041400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:48030800-48047200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:48030800-48048000	Strong transcription	Hela-S3	cervix
20	chr2:48030800-48049400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:48030800-48049600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:48030800-48067000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:48030800-48067000	Strong transcription	Fetal Thymus	thymus
24	chr2:48031000-48042400	Strong transcription	A549	lung
25	chr2:48031000-48049400	Strong transcription	Fetal Brain Female	brain
26	chr2:48031000-48053000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:48031000-48067000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:48031000-48067000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:48031000-48067200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:48031200-48048600	Strong transcription	K562	blood
31	chr2:48031200-48049600	Strong transcription	Primary B cells from cord blood	blood
32	chr2:48031200-48053800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:48031200-48065800	Strong transcription	Liver	Liver
34	chr2:48031200-48066800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:48031400-48042000	Weak transcription	Esophagus	oesophagus
36	chr2:48031400-48042800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:48031400-48042800	Weak transcription	Aorta	Aorta
38	chr2:48031400-48046400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:48031400-48050000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:48031400-48051400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:48031400-48060600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:48031400-48066800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:48031400-48067000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:48031400-48067800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:48031400-48067800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:48031400-48072600	Weak transcription	Stomach Mucosa	stomach
47	chr2:48032000-48043000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr2:48032000-48058000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:48032200-48042000	Weak transcription	Right Ventricle	heart
50	chr2:48032200-48042600	Weak transcription	Lung	lung

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