Variant report

Variant	rs13058138
Chromosome Location	chr22:31002638-31002639
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	POLR2A	chr22:31002471-31003513	HUVEC	blood vessel:	n/a	n/a
2	USF2	chr22:31002629-31002966	HepG2	liver:	n/a	n/a
3	SP4	chr22:31002502-31003158	H1-hESC	embryonic stem cell:	n/a	chr22:31002751-31002762 chr22:31002715-31002726
4	SP1	chr22:31002383-31003230	H1-hESC	embryonic stem cell:	n/a	chr22:31003148-31003162 chr22:31003147-31003159 chr22:31003148-31003158 chr22:31003144-31003153 chr22:31003148-31003157 chr22:31003143-31003152 chr22:31003147-31003159 chr22:31002751-31002762 chr22:31002715-31002726
5	POLR2A	chr22:31002632-31003514	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr22:31001849-31003651	HUVEC	blood vessel:	n/a	n/a
7	MAX	chr22:31002615-31003354	HUVEC	blood vessel:	n/a	n/a
8	MYC	chr22:31002536-31003352	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr22:31002519-31003330	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr22:31002555-31003250	A549	lung:	n/a	n/a
11	REST	chr22:31002402-31003757	H1-neurons	neurons:	n/a	chr22:31003257-31003270
12	USF1	chr22:31002550-31003278	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr22:31002198-31003605	H1-hESC	embryonic stem cell:	n/a	n/a
14	USF2	chr22:31002603-31003152	H1-hESC	embryonic stem cell:	n/a	n/a
15	USF1	chr22:31002493-31003283	HCT-116	colon:	n/a	n/a
16	TCF12	chr22:31002485-31003301	ECC-1	luminal epithelium:	n/a	n/a
17	TEAD4	chr22:31002604-31003253	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr22:31002583-31003419	H1-neurons	neurons:	n/a	n/a
19	USF2	chr22:31002615-31003002	GM12878	blood:	n/a	n/a
20	MAFK	chr22:31002630-31002993	H1-hESC	embryonic stem cell:	n/a	chr22:31002767-31002778 chr22:31002765-31002779
21	POLR2A	chr22:31002207-31003427	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr22:31002519-31003502	K562	blood:	n/a	n/a
23	ZNF143	chr22:31002410-31003204	H1-hESC	embryonic stem cell:	n/a	n/a
24	CEBPB	chr22:31002378-31003040	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr22:31002552-31003425	ECC-1	luminal epithelium:	n/a	n/a
26	USF1	chr22:31002508-31003271	H1-hESC	embryonic stem cell:	n/a	n/a
27	E2F6	chr22:31002504-31003341	H1-hESC	embryonic stem cell:	n/a	chr22:31003121-31003133
28	ZBTB7A	chr22:31002615-31002858	K562	blood:	n/a	n/a
29	USF1	chr22:31002594-31003055	A549	lung:	n/a	n/a
30	MAFK	chr22:31002633-31002969	K562	blood:	n/a	chr22:31002767-31002778 chr22:31002765-31002779
31	SIN3AK20	chr22:31002632-31003403	H1-hESC	embryonic stem cell:	n/a	n/a
32	USF1	chr22:31002562-31003231	SK-N-SH_RA	brain:	n/a	n/a
33	TEAD4	chr22:31002543-31003258	H1-hESC	embryonic stem cell:	n/a	n/a
34	MXI1	chr22:31002462-31003927	SK-N-SH	brain:	n/a	n/a
35	USF1	chr22:31002576-31003154	SK-N-SH_RA	brain:	n/a	n/a
36	SP1	chr22:31002602-31003307	A549	lung:	n/a	chr22:31003148-31003162 chr22:31003147-31003159 chr22:31003148-31003158 chr22:31003144-31003153 chr22:31003148-31003157 chr22:31003143-31003152 chr22:31003147-31003159 chr22:31002751-31002762 chr22:31002715-31002726
37	MAX	chr22:31002457-31003440	H1-hESC	embryonic stem cell:	n/a	n/a
38	CHD2	chr22:31002580-31003203	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr22:31002370-31003231	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr22:31002544-31003337	A549	lung:	n/a	n/a
41	USF1	chr22:31002533-31003208	H1-hESC	embryonic stem cell:	n/a	n/a
42	PBX3	chr22:31002583-31002985	A549	lung:	n/a	n/a
43	GTF2F1	chr22:31002515-31003201	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr22:31002552-31003469	H1-hESC	embryonic stem cell:	n/a	n/a
45	SP4	chr22:31002570-31003197	H1-hESC	embryonic stem cell:	n/a	chr22:31002751-31002762 chr22:31002715-31002726
46	BHLHE40	chr22:31002604-31003351	K562	blood:	n/a	n/a
47	E2F6	chr22:31002546-31003260	H1-hESC	embryonic stem cell:	n/a	chr22:31003121-31003133
48	EGR1	chr22:31002591-31002877	K562	blood:	n/a	n/a
49	ATF3	chr22:31002554-31002933	GM12878	blood:	n/a	n/a
50	RUNX3	chr22:31002601-31002919	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31001608..31004689-chr22:31008894..31012791,3	K562	blood:
2	chr22:30987737..30989936-chr22:31002004..31003702,2	MCF-7	breast:
3	chr22:30934256..30936381-chr22:31000054..31002763,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCN2-1	chr22:31002579-31002674	ENSG00000223831.1

Variant related genes	Relation type
TCN2	TF binding region
ENSG00000185339	Chromatin interaction
ENSG00000100029	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12160073	0.90[AMR][1000 genomes]
rs13056240	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34978834	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4343559	0.83[AMR][1000 genomes]
rs740234	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs757874	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30993200-31002800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:31001000-31002800	Enhancers	Stomach Mucosa	stomach
3	chr22:31001200-31002800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr22:31001400-31002800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr22:31001400-31002800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr22:31001400-31002800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr22:31001400-31003200	Enhancers	Spleen	Spleen
8	chr22:31001400-31003800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr22:31001400-31006400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr22:31001600-31002800	Enhancers	Primary B cells from peripheral blood	blood
11	chr22:31001600-31002800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr22:31001600-31002800	Weak transcription	Esophagus	oesophagus
13	chr22:31001600-31002800	Weak transcription	Gastric	stomach
14	chr22:31001600-31003200	Active TSS	Psoas Muscle	Psoas
15	chr22:31001800-31002800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:31001800-31002800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr22:31001800-31002800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr22:31001800-31002800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr22:31001800-31002800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr22:31001800-31003600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr22:31001800-31003600	Active TSS	Right Atrium	heart
22	chr22:31001800-31003800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr22:31001800-31004400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr22:31002000-31002800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr22:31002000-31002800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr22:31002000-31002800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr22:31002000-31002800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr22:31002000-31003000	Active TSS	Brain Substantia Nigra	brain
29	chr22:31002000-31003200	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr22:31002000-31003200	Active TSS	Rectal Smooth Muscle	rectum
31	chr22:31002000-31003400	Active TSS	Fetal Brain Female	brain
32	chr22:31002000-31007000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr22:31002200-31002800	Active TSS	H1 Cell Line	embryonic stem cell
34	chr22:31002200-31002800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr22:31002200-31002800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr22:31002200-31002800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr22:31002200-31002800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr22:31002200-31002800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr22:31002200-31002800	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr22:31002200-31002800	Enhancers	GM12878-XiMat	blood
41	chr22:31002200-31002800	Active TSS	NH-A	brain
42	chr22:31002200-31002800	Active TSS	NHDF-Ad	bronchial
43	chr22:31002200-31003200	Active TSS	Brain Anterior Caudate	brain
44	chr22:31002200-31003200	Active TSS	Fetal Intestine Large	intestine
45	chr22:31002200-31003200	Active TSS	Ovary	ovary
46	chr22:31002200-31003200	Active TSS	A549	lung
47	chr22:31002200-31003400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:31002200-31003400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr22:31002200-31003400	Active TSS	Brain Angular Gyrus	brain
50	chr22:31002200-31003400	Active TSS	Brain Germinal Matrix	brain

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