Variant report

Variant	rs2241845
Chromosome Location	chr2:111879100-111879101
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	STAT3	chr2:111879013-111879213	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr2:111878960-111879110	SAEC	small airway:	n/a	chr2:111878977-111878985
3	POLR2A	chr2:111878924-111879182	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr2:111877408-111879340	K562	blood:	n/a	chr2:111878414-111878423 chr2:111877747-111877759 chr2:111877478-111877490 chr2:111878679-111878691 chr2:111877963-111877973 chr2:111878285-111878294 chr2:111878171-111878181
5	PAX5	chr2:111878278-111879229	GM12878	blood:	n/a	chr2:111878388-111878397 chr2:111879173-111879182 chr2:111879020-111879029
6	MAX	chr2:111877563-111881015	NB4	blood:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
7	MAX	chr2:111877317-111879304	H1-hESC	embryonic stem cell:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111877479-111877489 chr2:111879218-111879227
8	E2F6	chr2:111876311-111880584	H1-hESC	embryonic stem cell:	n/a	chr2:111876443-111876455 chr2:111878414-111878423 chr2:111880549-111880558 chr2:111880095-111880104 chr2:111877747-111877759 chr2:111877347-111877357 chr2:111876622-111876632 chr2:111877478-111877490 chr2:111878679-111878691 chr2:111877963-111877973 chr2:111880318-111880330 chr2:111878285-111878294 chr2:111878171-111878181 chr2:111880053-111880060
9	POLR2A	chr2:111877782-111879129	MCF-7	breast:	n/a	n/a
10	MAX	chr2:111877825-111879196	SK-N-SH	brain:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693
11	TCF12	chr2:111877680-111880212	A549	lung:	n/a	n/a
12	SIN3AK20	chr2:111877611-111881217	MCF-7	breast:	n/a	n/a
13	CHD1	chr2:111878621-111881270	H1-hESC	embryonic stem cell:	n/a	chr2:111878901-111878911
14	MTA3	chr2:111878588-111879518	GM12878	blood:	n/a	n/a
15	PAX5	chr2:111878336-111879403	GM12878	blood:	n/a	chr2:111878388-111878397 chr2:111879173-111879182 chr2:111879020-111879029
16	TCF12	chr2:111877517-111879634	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr2:111877806-111880414	GM12878	blood:	n/a	n/a
18	HCFC1	chr2:111877979-111880854	K562	blood:	n/a	n/a
19	POLR2A	chr2:111877942-111881067	IMR90	lung:	n/a	n/a
20	POLR2A	chr2:111877963-111879180	K562	blood:	n/a	n/a
21	E2F6	chr2:111878578-111880256	A549	lung:	n/a	chr2:111880095-111880104 chr2:111878679-111878691 chr2:111880053-111880060
22	MAX	chr2:111877542-111881163	HepG2	liver:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
23	SPI1	chr2:111879095-111879351	HL-60	blood:	n/a	n/a
24	POLR2A	chr2:111877432-111881054	K562	blood:	n/a	n/a
25	POLR2A	chr2:111878117-111879345	H1-neurons	neurons:	n/a	n/a
26	TBL1XR1	chr2:111878781-111879135	GM12878	blood:	n/a	n/a
27	RELA	chr2:111878176-111879100	GM12892	blood:	n/a	n/a
28	MAX	chr2:111877713-111879368	A549	lung:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
29	SIN3AK20	chr2:111877957-111879169	HepG2	liver:	n/a	n/a
30	SMARCB1	chr2:111877080-111881031	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr2:111878112-111879219	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:111877652-111881216	H1-hESC	embryonic stem cell:	n/a	n/a
33	TEAD4	chr2:111878850-111879341	K562	blood:	n/a	n/a
34	MYC	chr2:111877906-111880742	K562	blood:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
35	ZKSCAN1	chr2:111878027-111879455	Hela-S3	cervix:	n/a	n/a
36	E2F6	chr2:111877723-111880882	Hela-S3	cervix:	n/a	chr2:111878414-111878423 chr2:111880549-111880558 chr2:111880095-111880104 chr2:111877747-111877759 chr2:111878679-111878691 chr2:111877963-111877973 chr2:111880318-111880330 chr2:111878285-111878294 chr2:111878171-111878181 chr2:111880053-111880060
37	POLR2A	chr2:111877744-111880423	NB4	blood:	n/a	n/a
38	MYC	chr2:111877505-111879474	K562	blood:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
39	TBP	chr2:111877793-111879385	K562	blood:	n/a	n/a
40	MYC	chr2:111877859-111879233	Hela-S3	cervix:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
41	MAZ	chr2:111877230-111879730	GM12878	blood:	n/a	chr2:111878235-111878244 chr2:111878683-111878693 chr2:111877479-111877489 chr2:111879218-111879227
42	EP300	chr2:111878004-111879296	HepG2	liver:	n/a	chr2:111878469-111878485 chr2:111878110-111878126 chr2:111879145-111879154 chr2:111878390-111878406 chr2:111879080-111879089 chr2:111878168-111878177 chr2:111878159-111878175 chr2:111878171-111878180
43	UBTF	chr2:111877688-111881146	K562	blood:	n/a	n/a
44	CHD2	chr2:111877705-111879159	Hela-S3	cervix:	n/a	chr2:111878005-111878015 chr2:111878901-111878911
45	MXI1	chr2:111877406-111881885	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr2:111878954-111879222	Hela-S3	cervix:	n/a	n/a
47	E2F6	chr2:111877377-111879315	H1-hESC	embryonic stem cell:	n/a	chr2:111878414-111878423 chr2:111877747-111877759 chr2:111877478-111877490 chr2:111878679-111878691 chr2:111877963-111877973 chr2:111878285-111878294 chr2:111878171-111878181
48	BHLHE40	chr2:111877526-111880906	K562	blood:	n/a	chr2:111878164-111878180 chr2:111878158-111878174 chr2:111879083-111879099 chr2:111878389-111878405 chr2:111880077-111880093 chr2:111878166-111878182 chr2:111879143-111879159
49	POLR2A	chr2:111877703-111879109	GM12892	blood:	n/a	n/a
50	SIN3AK20	chr2:111877950-111881096	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:111869458..111872537-chr2:111876483..111880583,5	MCF-7	breast:
2	chr2:111877393..111879713-chr2:112235053..112237981,2	K562	blood:
3	chr2:111434111..111436826-chr2:111878321..111880919,2	K562	blood:
4	chr2:111876826..111879311-chr2:111966028..111968773,2	K562	blood:
5	chr12:28120103..28122878-chr2:111877498..111879183,2	MCF-7	breast:

Variant related genes	Relation type
BCL2L11	TF binding region
ENSG00000172965	Chromatin interaction
ENSG00000087494	Chromatin interaction
ENSG00000169679	Chromatin interaction
ENSG00000204581	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10204044	0.82[ASW][hapmap]
rs13396983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17558117	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs1877331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1980045	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2015454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241843	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36018702	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3827536	0.96[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4848393	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849417	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849442	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs590097	0.84[ASW][hapmap]
rs616084	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs616130	0.84[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs616582	0.85[CEU][hapmap]
rs6542334	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6746608	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6750599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6753785	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6758181	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676119	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7567444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9308731	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv874842	chr2:111870220-111892984	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv829618	chr2:111875627-111881547	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	esv3338590	chr2:111876081-111880479	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv3373707	chr2:111877306-111879854	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2241845	BCL2L11	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111874400-111879800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr2:111874800-111879600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:111874800-111880000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:111875200-111880000	Bivalent Enhancer	Fetal Brain Male	brain
5	chr2:111875600-111880000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:111875600-111881200	Active TSS	Psoas Muscle	Psoas
7	chr2:111876200-111880000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:111876400-111880000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:111877000-111881000	Active TSS	Small Intestine	intestine
10	chr2:111877000-111881400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:111877200-111879200	Active TSS	Rectal Smooth Muscle	rectum
12	chr2:111877200-111880800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:111877400-111879200	Transcr. at gene 5' and 3'	Right Atrium	heart
14	chr2:111877600-111879200	Active TSS	Brain Cingulate Gyrus	brain
15	chr2:111877600-111879200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr2:111877600-111879400	Active TSS	HSMM	muscle
17	chr2:111877600-111879800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:111877600-111881000	Active TSS	Esophagus	oesophagus
19	chr2:111877600-111881200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:111877600-111881200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:111877600-111881400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:111877800-111879200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr2:111877800-111879200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:111877800-111879200	Active TSS	Brain Angular Gyrus	brain
25	chr2:111877800-111879200	Active TSS	Placenta Amnion	Placenta Amnion
26	chr2:111877800-111879200	Active TSS	K562	blood
27	chr2:111877800-111879400	Active TSS	Fetal Heart	heart
28	chr2:111877800-111880000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
29	chr2:111877800-111880800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:111877800-111881000	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr2:111877800-111881000	Active TSS	A549	lung
32	chr2:111877800-111881000	Active TSS	Hela-S3	cervix
33	chr2:111877800-111881200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr2:111877800-111881400	Active TSS	Ovary	ovary
35	chr2:111877800-111881400	Active TSS	HSMMtube	muscle
36	chr2:111878000-111879200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:111878000-111879200	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr2:111878000-111879200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:111878000-111879400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
40	chr2:111878000-111879400	Active TSS	Primary B cells from peripheral blood	blood
41	chr2:111878000-111879400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
42	chr2:111878000-111879400	Active TSS	Fetal Intestine Small	intestine
43	chr2:111878000-111879400	Active TSS	NHEK	skin
44	chr2:111878000-111879600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:111878000-111879600	Bivalent/Poised TSS	Fetal Thymus	thymus
46	chr2:111878000-111879600	Active TSS	Lung	lung
47	chr2:111878000-111879600	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr2:111878000-111880400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr2:111878000-111880800	Active TSS	Primary T cells from cord blood	blood
50	chr2:111878000-111881000	Active TSS	Primary T killer memory cells from peripheral blood	blood

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