Variant report

Variant	rs1402048
Chromosome Location	chr2:30978916-30978917
allele	A/G
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	JUND	chr2:30978642-30979472	MCF-7	breast:	n/a	chr2:30978880-30978889 chr2:30979219-30979228 chr2:30978923-30978934 chr2:30979221-30979228 chr2:30979218-30979229
2	FOXA1	chr2:30978822-30979154	T-47D	breast:	n/a	n/a
3	EP300	chr2:30978784-30979110	T-47D	breast:	n/a	chr2:30979063-30979070
4	ZNF217	chr2:30978816-30979369	MCF-7	breast:	n/a	n/a
5	YY1	chr2:30978846-30979193	SK-N-SH_RA	brain:	n/a	n/a
6	YY1	chr2:30978889-30979093	K562	blood:	n/a	n/a
7	GATA3	chr2:30978846-30979431	MCF-7	breast:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
8	ELF1	chr2:30978864-30979268	K562	blood:	n/a	chr2:30979061-30979074 chr2:30979062-30979073 chr2:30979063-30979072
9	SRF	chr2:30978653-30979587	MCF-7	breast:	n/a	n/a
10	GATA2	chr2:30978817-30980069	SH-SY5Y	brain:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
11	SIN3AK20	chr2:30978539-30979598	MCF-7	breast:	n/a	n/a
12	YY1	chr2:30978829-30979373	SK-N-SH_RA	brain:	n/a	n/a
13	GATA3	chr2:30978818-30979425	T-47D	breast:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
14	FOSL2	chr2:30978710-30979499	MCF-7	breast:	n/a	chr2:30978880-30978889 chr2:30979219-30979228 chr2:30978923-30978934 chr2:30979221-30979228 chr2:30979219-30979230
15	JUND	chr2:30978681-30979750	SK-N-SH	brain:	n/a	chr2:30978880-30978889 chr2:30979219-30979228 chr2:30978923-30978934 chr2:30979221-30979228 chr2:30979218-30979229
16	EP300	chr2:30978817-30979378	SK-N-SH_RA	brain:	n/a	chr2:30979219-30979228 chr2:30979063-30979070
17	GATA3	chr2:30978476-30979448	SH-SY5Y	brain:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
18	JUND	chr2:30978890-30979435	T-47D	breast:	n/a	chr2:30979219-30979228 chr2:30978923-30978934 chr2:30979221-30979228 chr2:30979218-30979229
19	ELF1	chr2:30978744-30979569	MCF-7	breast:	n/a	chr2:30979061-30979074 chr2:30979062-30979073 chr2:30979063-30979072
20	GABPA	chr2:30978636-30979482	MCF-7	breast:	n/a	n/a
21	FOXA1	chr2:30978774-30979188	T-47D	breast:	n/a	n/a
22	GABPA	chr2:30978874-30979256	K562	blood:	n/a	n/a
23	MXI1	chr2:30978593-30979867	SK-N-SH	brain:	n/a	n/a
24	EP300	chr2:30978805-30979265	T-47D	breast:	n/a	chr2:30979219-30979228 chr2:30979063-30979070
25	EP300	chr2:30978394-30980285	SK-N-SH	brain:	n/a	chr2:30979544-30979558 chr2:30979219-30979228 chr2:30979063-30979070
26	GATA3	chr2:30978838-30979452	SK-N-SH	brain:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
27	FOSL2	chr2:30978749-30979496	MCF-7	breast:	n/a	chr2:30978880-30978889 chr2:30979219-30979228 chr2:30978923-30978934 chr2:30979221-30979228 chr2:30979219-30979230
28	NR2F2	chr2:30978661-30979430	MCF-7	breast:	n/a	n/a
29	MAX	chr2:30978654-30979479	MCF-7	breast:	n/a	n/a
30	EP300	chr2:30978759-30979291	MCF-7	breast:	n/a	chr2:30979219-30979228 chr2:30979063-30979070
31	ELF1	chr2:30978718-30979501	MCF-7	breast:	n/a	chr2:30979061-30979074 chr2:30979062-30979073 chr2:30979063-30979072
32	HDAC2	chr2:30978829-30979380	MCF-7	breast:	n/a	n/a
33	KAP1	chr2:30978893-30979386	HEK293	kidney:	n/a	n/a
34	GATA3	chr2:30978629-30979550	MCF-7	breast:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
35	TEAD4	chr2:30978866-30979421	K562	blood:	n/a	n/a
36	GATA3	chr2:30978831-30979342	T-47D	breast:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
37	EP300	chr2:30978840-30979340	SK-N-SH_RA	brain:	n/a	chr2:30979219-30979228 chr2:30979063-30979070
38	GATA1	chr2:30978892-30979439	K562	blood:	n/a	chr2:30979221-30979230
39	GATA3	chr2:30978530-30979654	MCF-7	breast:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
40	CCNT2	chr2:30978893-30979241	K562	blood:	n/a	n/a
41	NR2F2	chr2:30978600-30980160	MCF-7	breast:	n/a	n/a
42	GABPA	chr2:30978715-30979457	MCF-7	breast:	n/a	n/a
43	TCF7L2	chr2:30978741-30979350	MCF-7	breast:	n/a	n/a
44	JUN	chr2:30978854-30979554	K562	blood:	n/a	chr2:30978880-30978889 chr2:30979219-30979228 chr2:30978923-30978934 chr2:30979221-30979228

No.	Distal block	Cell Line	Cell type
1	chr2:30974357..30976391-chr2:30976860..30980887,3	K562	blood:
2	chr2:30971328..30973922-chr2:30977969..30979743,3	MCF-7	breast:
3	chr2:30974420..30976391-chr2:30977915..30980887,2	K562	blood:
4	chr2:30977562..30982184-chr2:31026694..31034377,7	MCF-7	breast:
5	chr2:30967775..30969478-chr2:30977702..30980114,2	MCF-7	breast:
6	chr2:30977154..30980117-chr2:31067172..31070017,2	MCF-7	breast:
7	chr2:30978342..30980549-chr2:31003793..31005445,2	MCF-7	breast:
8	chr2:30978882..30982474-chr2:30994656..30997998,4	MCF-7	breast:

Variant related genes	Relation type
CAPN13	TF binding region
ENSG00000162949	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2276567	0.85[CEU][hapmap]
rs2609932	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2681676	0.90[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2926303	0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs479103	0.89[GIH][hapmap]
rs482384	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs485100	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs508405	0.84[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs939368	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
2	nsv873770	chr2:30952987-30984850	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv520269	chr2:30958137-30988375	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv456019	chr2:30968228-30984850	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv581267	chr2:30968228-30984850	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1402048	C2orf53	cis	cerebellum	SCAN
rs1402048	PLB1	cis	cerebellum	SCAN
rs1402048	C2orf28	cis	parietal	SCAN
rs1402048	CAD	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30960400-30980000	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:30965800-30999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:30968200-30985600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:30971000-30984800	Weak transcription	Stomach Mucosa	stomach
5	chr2:30977800-30979200	Weak transcription	Gastric	stomach
6	chr2:30978000-30980800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:30978200-30979000	Enhancers	Spleen	Spleen
8	chr2:30978200-30980000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:30978200-30980200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:30978400-30979200	Enhancers	Lung	lung
11	chr2:30978400-30979400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:30978400-30979600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr2:30978400-30980800	Enhancers	Pancreas	Pancrea
14	chr2:30978400-30981200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:30978600-30979200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr2:30978600-30979400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:30978600-30979600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr2:30978600-30979600	Enhancers	HMEC	breast
19	chr2:30978600-30979800	Enhancers	NHEK	skin
20	chr2:30978600-30984600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:30978800-30979000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:30978800-30979000	Enhancers	Fetal Intestine Small	intestine
23	chr2:30978800-30979200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:30978800-30979200	Enhancers	Adipose Nuclei	Adipose
25	chr2:30978800-30979200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr2:30978800-30979400	Enhancers	Fetal Lung	lung
27	chr2:30978800-30979600	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:30978800-30979600	Enhancers	Esophagus	oesophagus
29	chr2:30978800-30979600	Enhancers	Fetal Intestine Large	intestine
30	chr2:30978800-30979600	Enhancers	Placenta	Placenta
31	chr2:30978800-30979600	Enhancers	K562	blood
32	chr2:30978800-30979800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr2:30978800-30979800	Enhancers	Small Intestine	intestine
34	chr2:30978800-30980200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:30978800-30980200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr2:30978800-30980600	Enhancers	Fetal Muscle Leg	muscle
37	chr2:30978800-30980600	Strong transcription	Rectal Mucosa Donor 31	rectum

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