Variant report

Variant	rs1916
Chromosome Location	chr22:31892121-31892122
allele	C/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	BCLAF1	chr22:31891896-31892711	GM12878	blood:	n/a	chr22:31892187-31892200 chr22:31892122-31892131 chr22:31892191-31892204
2	POLR2A	chr22:31891857-31893265	GM12892	blood:	n/a	n/a
3	POLR2A	chr22:31891980-31892848	ECC-1	luminal epithelium:	n/a	n/a
4	PML	chr22:31891962-31892565	GM12878	blood:	n/a	n/a
5	RUNX3	chr22:31891860-31894008	GM12878	blood:	n/a	n/a
6	HCFC1	chr22:31891851-31892646	K562	blood:	n/a	n/a
7	ELK1	chr22:31892028-31892247	K562	blood:	n/a	chr22:31892122-31892131 chr22:31892122-31892131
8	GTF2F1	chr22:31892023-31892655	Hela-S3	cervix:	n/a	chr22:31892246-31892257
9	MAZ	chr22:31891683-31892958	GM12878	blood:	n/a	chr22:31891799-31891810 chr22:31891799-31891810
10	ELF1	chr22:31891941-31892585	K562	blood:	n/a	chr22:31892120-31892131
11	FOXM1	chr22:31891888-31892932	GM12878	blood:	n/a	n/a
12	HA-E2F1	chr22:31891997-31893145	MCF-7	breast:	n/a	chr22:31892506-31892517 chr22:31892849-31892861
13	ARID3A	chr22:31891935-31892132	K562	blood:	n/a	n/a
14	TBP	chr22:31891781-31892634	Hela-S3	cervix:	n/a	chr22:31892246-31892257
15	POLR2A	chr22:31891653-31892770	MCF10A-Er-Src	breast:	n/a	n/a
16	EGR1	chr22:31892029-31892233	GM12878	blood:	n/a	chr22:31892106-31892119 chr22:31892122-31892131 chr22:31892107-31892117
17	MYC	chr22:31892068-31892226	HepG2	liver:	n/a	n/a
18	CUX1	chr22:31891950-31892246	K562	blood:	n/a	n/a
19	TAF1	chr22:31892057-31892405	GM12891	blood:	n/a	n/a
20	ELF1	chr22:31891889-31892343	HepG2	liver:	n/a	chr22:31892120-31892131
21	POLR2A	chr22:31891849-31892856	HepG2	liver:	n/a	n/a
22	POLR2A	chr22:31891843-31892865	HL-60	blood:	n/a	n/a
23	TCF12	chr22:31891894-31892874	A549	lung:	n/a	chr22:31891971-31891979
24	POLR2A	chr22:31891899-31893258	GM12892	blood:	n/a	n/a
25	POU2F2	chr22:31891948-31892471	GM12891	blood:	n/a	n/a
26	TCF12	chr22:31891884-31892646	ECC-1	luminal epithelium:	n/a	chr22:31891971-31891979
27	POLR2A	chr22:31891963-31892725	A549	lung:	n/a	n/a
28	EGR1	chr22:31891942-31892223	K562	blood:	n/a	chr22:31892106-31892119 chr22:31892122-31892131 chr22:31892107-31892117
29	SIN3AK20	chr22:31891909-31892816	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr22:31891935-31892746	HUVEC	blood vessel:	n/a	n/a
31	TAF1	chr22:31892061-31892847	H1-neurons	neurons:	n/a	n/a
32	RUNX3	chr22:31891878-31893271	GM12878	blood:	n/a	n/a
33	CEBPB	chr22:31891827-31892782	GM12878	blood:	n/a	n/a
34	GABPA	chr22:31891863-31893094	MCF-7	breast:	n/a	chr22:31892195-31892204
35	POU2F2	chr22:31891951-31892483	GM12878	blood:	n/a	n/a
36	TEAD4	chr22:31891915-31892389	ECC-1	luminal epithelium:	n/a	n/a
37	SP1	chr22:31891916-31892490	GM12878	blood:	n/a	chr22:31892339-31892349 chr22:31892433-31892442 chr22:31892433-31892442 chr22:31892432-31892441
38	MAX	chr22:31891853-31893057	SK-N-SH	brain:	n/a	n/a
39	E2F6	chr22:31892083-31892953	H1-hESC	embryonic stem cell:	n/a	chr22:31892849-31892861
40	TFAP2C	chr22:31892053-31893176	Hela-S3	cervix:	n/a	chr22:31892882-31892897
41	POLR2A	chr22:31891875-31893504	Raji	blood:	n/a	n/a
42	KAP1	chr22:31892075-31893835	HEK293	kidney:	n/a	n/a
43	CEBPB	chr22:31892031-31892569	Hela-S3	cervix:	n/a	n/a
44	ELF1	chr22:31891912-31893036	GM12878	blood:	n/a	chr22:31892120-31892131
45	TAF1	chr22:31892110-31892506	K562	blood:	n/a	n/a
46	E2F6	chr22:31892018-31892703	K562	blood:	n/a	n/a
47	BCL3	chr22:31891880-31892610	GM12878	blood:	n/a	chr22:31892187-31892200 chr22:31892122-31892131 chr22:31892191-31892204
48	POLR2A	chr22:31891931-31892830	A549	lung:	n/a	n/a
49	EGR1	chr22:31891948-31892353	GM12878	blood:	n/a	chr22:31892106-31892119 chr22:31892122-31892131 chr22:31892107-31892117
50	MAX	chr22:31891938-31892805	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:31892074-31892124	BE2_C	brain:	n/a
2	chr22:31892074-31892124	PrEC	prostate:	n/a
3	chr22:31892114-31892164	HMEC	breast:	n/a
4	chr22:31892114-31892164	RPTEC	kidney:	n/a
5	chr22:31892074-31892124	K562	blood:	n/a
6	chr22:31892074-31892124	GM19239	blood:	n/a
7	chr22:31892114-31892164	SAEC	small airway:	n/a
8	chr22:31892074-31892124	HRPEpiC	eye:	n/a
9	chr22:31892074-31892124	CMK	blood:	n/a
10	chr22:31892114-31892164	Caco-2	colon:	n/a
11	chr22:31892114-31892164	Hepatocyte	liver:	n/a
12	chr22:31892114-31892164	HCF	heart:	n/a
13	chr22:31892074-31892124	BJ	skin:	n/a
14	chr22:31892074-31892124	Caco-2	colon:	n/a
15	chr22:31892114-31892164	H1-hESC	embryonic stem cell:	embryo
16	chr22:31892114-31892164	A549	lung:	n/a
17	chr22:31892114-31892164	HCPEpiC	choroid plexus:	n/a
18	chr22:31892074-31892124	IMR90	lung:	fetal
19	chr22:31892074-31892124	NH-A	brain:	n/a
20	chr22:31892074-31892124	LNCaP	prostate:	n/a
21	chr22:31892114-31892164	GM12878	blood:	n/a
22	chr22:31892114-31892164	NHDF-neo	bronchial:	n/a
23	chr22:31892114-31892164	HUVEC	blood vessel:	n/a
24	chr22:31892114-31892164	ovcar-3	ovarian:	n/a
25	chr22:31892114-31892164	HIPEpiC	eye:	n/a
26	chr22:31892074-31892124	AG09319	gingival:	n/a
27	chr22:31892114-31892164	MCF10A-Er-Src	breast:	n/a
28	chr22:31892074-31892124	HL-60	blood:	n/a
29	chr22:31892074-31892124	ProgFib	skin:	n/a
30	chr22:31892114-31892164	PrEC	prostate:	n/a
31	chr22:31892114-31892164	HRPEpiC	eye:	n/a
32	chr22:31892114-31892164	HPAEpiC	pulmonary alveolar:	n/a
33	chr22:31892114-31892164	AG04449	skin:	fetal
34	chr22:31892114-31892164	HepG2	liver:	n/a
35	chr22:31892074-31892124	A549	lung:	n/a
36	chr22:31892074-31892124	Hela-S3	cervix:	n/a
37	chr22:31892114-31892164	T-47D	breast:	n/a
38	chr22:31892114-31892164	GM06990	blood:	n/a
39	chr22:31892074-31892124	HMEC	breast:	n/a
40	chr22:31892074-31892124	Jurkat	blood:	n/a
41	chr22:31892074-31892124	Hepatocyte	liver:	n/a
42	chr22:31892074-31892124	HPAEpiC	pulmonary alveolar:	n/a
43	chr22:31892114-31892164	CMK	blood:	n/a
44	chr22:31892114-31892164	SK-N-MC	brain:	n/a
45	chr22:31892074-31892124	NT2-D1	testis:	n/a
46	chr22:31892074-31892124	HUVEC	blood vessel:	n/a
47	chr22:31892114-31892164	ProgFib	skin:	n/a
48	chr22:31892074-31892124	HIPEpiC	eye:	n/a
49	chr22:31892074-31892124	ECC-1	luminal epithelium:	n/a
50	chr22:31892074-31892124	SK-N-MC	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31891360..31893218-chr22:32058204..32060412,2	MCF-7	breast:
2	chr22:31890586..31892478-chr6:26238591..26241305,2	MCF-7	breast:
3	chr22:31849740..31852347-chr22:31891078..31892965,2	K562	blood:
4	chr22:31890350..31892385-chr22:32144551..32147460,2	K562	blood:

Variant related genes	Relation type
SFI1	TF binding region
EIF4ENIF1	TF binding region
SFI1	CpG island
EIF4ENIF1	CpG island
ENSG00000240591	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000183530	Chromatin interaction
ENSG00000198327	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1543416	0.85[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs2006771	1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]
rs2012451	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap]
rs2103853	0.82[CHB][hapmap]
rs4541328	0.80[AMR][1000 genomes]
rs4820048	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap]
rs4820974	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap]
rs4820983	0.88[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap]
rs5753625	0.82[CHB][hapmap]
rs5753630	0.82[CHB][hapmap]
rs5753686	0.86[MKK][hapmap]
rs5994397	0.82[YRI][hapmap]
rs5997988	0.83[ASW][hapmap];0.85[CEU][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs5998002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs5998004	0.84[AMR][1000 genomes]
rs5998012	0.82[AMR][1000 genomes]
rs5998021	1.00[CEU][hapmap]
rs5998042	0.83[MKK][hapmap]
rs6518745	0.81[LWK][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap]
rs7287937	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs7289941	1.00[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap]
rs926928	0.80[LWK][hapmap];0.84[MKK][hapmap]

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	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1060776	chr22:31869892-31900359	Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3334530	chr22:31889221-31909085	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31891200-31893200	Active TSS	K562	blood
2	chr22:31891400-31892200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr22:31891400-31892200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr22:31891400-31892200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr22:31891400-31892400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr22:31891400-31892400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr22:31891400-31893000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:31891400-31893000	Active TSS	Brain Angular Gyrus	brain
9	chr22:31891400-31893000	Active TSS	Brain Anterior Caudate	brain
10	chr22:31891400-31893000	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr22:31891400-31893200	Active TSS	NHEK	skin
12	chr22:31891400-31893400	Active TSS	Hela-S3	cervix
13	chr22:31891600-31892200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr22:31891600-31892200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr22:31891600-31892200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr22:31891600-31892200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr22:31891600-31892200	Flanking Active TSS	HUVEC	blood vessel
18	chr22:31891600-31892400	Active TSS	Brain Germinal Matrix	brain
19	chr22:31891600-31892600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr22:31891600-31892600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr22:31891600-31892800	Active TSS	Right Ventricle	heart
22	chr22:31891600-31892800	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr22:31891600-31892800	Active TSS	Stomach Smooth Muscle	stomach
24	chr22:31891600-31893000	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr22:31891600-31893000	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr22:31891600-31893000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr22:31891600-31893000	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr22:31891600-31893000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr22:31891600-31893000	Active TSS	Fetal Brain Female	brain
30	chr22:31891600-31893000	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr22:31891600-31893000	Active TSS	Rectal Smooth Muscle	rectum
32	chr22:31891600-31893200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr22:31891600-31893200	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr22:31891600-31893200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr22:31891600-31893200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr22:31891600-31893200	Active TSS	Fetal Intestine Small	intestine
37	chr22:31891600-31893200	Active TSS	HSMMtube	muscle
38	chr22:31891600-31893400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:31891600-31893400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr22:31891600-31893400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr22:31891600-31893400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr22:31891600-31893400	Active TSS	Thymus	Thymus
43	chr22:31891600-31893400	Active TSS	HSMM	muscle
44	chr22:31891600-31893600	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr22:31891600-31893600	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr22:31891600-31893600	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr22:31891600-31893600	Active TSS	A549	lung
48	chr22:31891600-31893600	Active TSS	NHDF-Ad	bronchial
49	chr22:31891600-31893600	Active TSS	NHLF	lung
50	chr22:31891600-31893600	Active TSS	Osteobl	bone

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