Variant report

Variant	rs2609932
Chromosome Location	chr2:30979083-30979084
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	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	GABPA	chr2:30978930-30979270	K562	blood:	n/a	n/a
4	GABPA	chr2:30978967-30979391	SK-N-SH	brain:	n/a	n/a
5	EP300	chr2:30978784-30979110	T-47D	breast:	n/a	chr2:30979063-30979070
6	ZNF217	chr2:30978816-30979369	MCF-7	breast:	n/a	n/a
7	YY1	chr2:30978846-30979193	SK-N-SH_RA	brain:	n/a	n/a
8	GATA2	chr2:30979000-30979336	K562	blood:	n/a	chr2:30979221-30979230
9	YY1	chr2:30978889-30979093	K562	blood:	n/a	n/a
10	FOSL2	chr2:30979046-30979329	HepG2	liver:	n/a	chr2:30979219-30979228 chr2:30979221-30979228 chr2:30979219-30979230
11	GATA3	chr2:30978846-30979431	MCF-7	breast:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
12	EP300	chr2:30978996-30979370	K562	blood:	n/a	chr2:30979219-30979228 chr2:30979063-30979070
13	UBTF	chr2:30979041-30979271	K562	blood:	n/a	n/a
14	ELF1	chr2:30978864-30979268	K562	blood:	n/a	chr2:30979061-30979074 chr2:30979062-30979073 chr2:30979063-30979072
15	SRF	chr2:30978653-30979587	MCF-7	breast:	n/a	n/a
16	HCFC1	chr2:30978999-30979327	K562	blood:	n/a	n/a
17	GATA2	chr2:30978817-30980069	SH-SY5Y	brain:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
18	SIN3AK20	chr2:30978539-30979598	MCF-7	breast:	n/a	n/a
19	YY1	chr2:30978829-30979373	SK-N-SH_RA	brain:	n/a	n/a
20	GATA2	chr2:30979053-30979348	HUVEC	blood vessel:	n/a	chr2:30979221-30979230
21	TRIM28	chr2:30979036-30979244	K562	blood:	n/a	n/a
22	PML	chr2:30978960-30979301	K562	blood:	n/a	n/a
23	GATA3	chr2:30978818-30979425	T-47D	breast:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
24	FOSL1	chr2:30978952-30979368	K562	blood:	n/a	chr2:30979218-30979229 chr2:30979219-30979228 chr2:30979221-30979228
25	FOSL2	chr2:30978985-30979363	HepG2	liver:	n/a	chr2:30979219-30979228 chr2:30979221-30979228 chr2:30979219-30979230
26	FOS	chr2:30979078-30979337	MCF10A-Er-Src	breast:	n/a	chr2:30979219-30979228 chr2:30979221-30979228
27	TEAD4	chr2:30978984-30979336	K562	blood:	n/a	n/a
28	FOSL2	chr2:30978710-30979499	MCF-7	breast:	n/a	chr2:30978880-30978889 chr2:30979219-30979228 chr2:30978923-30978934 chr2:30979221-30979228 chr2:30979219-30979230
29	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
30	MAZ	chr2:30979033-30979363	K562	blood:	n/a	n/a
31	ATF3	chr2:30978993-30979413	K562	blood:	n/a	n/a
32	EP300	chr2:30978817-30979378	SK-N-SH_RA	brain:	n/a	chr2:30979219-30979228 chr2:30979063-30979070
33	JUN	chr2:30979028-30979404	K562	blood:	n/a	chr2:30979219-30979228 chr2:30979221-30979228
34	GATA3	chr2:30978476-30979448	SH-SY5Y	brain:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
35	JUND	chr2:30978890-30979435	T-47D	breast:	n/a	chr2:30979219-30979228 chr2:30978923-30978934 chr2:30979221-30979228 chr2:30979218-30979229
36	UBTF	chr2:30978981-30979304	K562	blood:	n/a	n/a
37	JUN	chr2:30979028-30979374	K562	blood:	n/a	chr2:30979219-30979228 chr2:30979221-30979228
38	ELF1	chr2:30978744-30979569	MCF-7	breast:	n/a	chr2:30979061-30979074 chr2:30979062-30979073 chr2:30979063-30979072
39	RAD21	chr2:30978923-30979367	SK-N-SH_RA	brain:	n/a	n/a
40	CBX3	chr2:30978961-30979339	K562	blood:	n/a	n/a
41	GABPA	chr2:30978636-30979482	MCF-7	breast:	n/a	n/a
42	FOXA1	chr2:30978774-30979188	T-47D	breast:	n/a	n/a
43	GABPA	chr2:30978874-30979256	K562	blood:	n/a	n/a
44	ATF1	chr2:30979033-30979379	K562	blood:	n/a	n/a
45	MXI1	chr2:30978593-30979867	SK-N-SH	brain:	n/a	n/a
46	JUND	chr2:30978966-30979422	K562	blood:	n/a	chr2:30979219-30979228 chr2:30979221-30979228 chr2:30979218-30979229
47	EP300	chr2:30978805-30979265	T-47D	breast:	n/a	chr2:30979219-30979228 chr2:30979063-30979070
48	EP300	chr2:30978394-30980285	SK-N-SH	brain:	n/a	chr2:30979544-30979558 chr2:30979219-30979228 chr2:30979063-30979070
49	GATA3	chr2:30978838-30979452	SK-N-SH	brain:	n/a	chr2:30979221-30979230 chr2:30978880-30978890
50	FOSL2	chr2:30978749-30979496	MCF-7	breast:	n/a	chr2:30978880-30978889 chr2:30979219-30979228 chr2:30978923-30978934 chr2:30979221-30979228 chr2:30979219-30979230

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: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1402048	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]
rs2276567	0.86[CEU][hapmap]
rs2681676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs2926303	0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs482384	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs485100	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs508405	0.94[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs939368	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[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

No data

Chromatin state (count:43 , 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	chr2:30978200-30980000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:30978200-30980200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:30978400-30979200	Enhancers	Lung	lung
10	chr2:30978400-30979400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:30978400-30979600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr2:30978400-30980800	Enhancers	Pancreas	Pancrea
13	chr2:30978400-30981200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:30978600-30979200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr2:30978600-30979400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:30978600-30979600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr2:30978600-30979600	Enhancers	HMEC	breast
18	chr2:30978600-30979800	Enhancers	NHEK	skin
19	chr2:30978600-30984600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:30978800-30979200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:30978800-30979200	Enhancers	Adipose Nuclei	Adipose
22	chr2:30978800-30979200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr2:30978800-30979400	Enhancers	Fetal Lung	lung
24	chr2:30978800-30979600	Enhancers	Duodenum Mucosa	Duodenum
25	chr2:30978800-30979600	Enhancers	Esophagus	oesophagus
26	chr2:30978800-30979600	Enhancers	Fetal Intestine Large	intestine
27	chr2:30978800-30979600	Enhancers	Placenta	Placenta
28	chr2:30978800-30979600	Enhancers	K562	blood
29	chr2:30978800-30979800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:30978800-30979800	Enhancers	Small Intestine	intestine
31	chr2:30978800-30980200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:30978800-30980200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
33	chr2:30978800-30980600	Enhancers	Fetal Muscle Leg	muscle
34	chr2:30978800-30980600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr2:30979000-30979200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:30979000-30979200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:30979000-30979200	Genic enhancers	Fetal Intestine Small	intestine
38	chr2:30979000-30979600	Enhancers	NHDF-Ad	bronchial
39	chr2:30979000-30979800	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr2:30979000-30979800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:30979000-30980000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:30979000-30980400	Weak transcription	Spleen	Spleen
43	chr2:30979000-30980600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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