Variant report

Variant	rs7997110
Chromosome Location	chr13:49107241-49107242
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	TAF1	chr13:49106247-49107412	GM12878	blood:	n/a	n/a
2	RELA	chr13:49104593-49107295	GM10847	blood:	n/a	n/a
3	PAX5	chr13:49107083-49107431	GM12878	blood:	n/a	n/a
4	ZNF143	chr13:49106418-49107333	H1-hESC	embryonic stem cell:	n/a	chr13:49106558-49106576 chr13:49107057-49107075
5	POLR2A	chr13:49105321-49107960	GM12878	blood:	n/a	n/a
6	RELA	chr13:49104753-49107644	GM15510	blood:	n/a	n/a
7	CTCF	chr13:49107177-49107322	GM19240	blood:	n/a	n/a
8	POLR2A	chr13:49106402-49107438	GM12878	blood:	n/a	n/a
9	CTCF	chr13:49107160-49107310	BJ	skin:	n/a	n/a
10	MAX	chr13:49107111-49107315	K562	blood:	n/a	n/a
11	POU2F2	chr13:49106447-49107382	GM12878	blood:	n/a	n/a
12	PAX5	chr13:49106446-49107494	GM12878	blood:	n/a	n/a
13	RCOR1	chr13:49106507-49107318	GM12878	blood:	n/a	n/a
14	POLR2A	chr13:49105879-49107776	SK-N-MC	brain:	n/a	n/a
15	JUND	chr13:49106643-49107255	K562	blood:	n/a	n/a
16	POLR2A	chr13:49106417-49107442	HUVEC	blood vessel:	n/a	n/a
17	CHD2	chr13:49107060-49107359	H1-hESC	embryonic stem cell:	n/a	chr13:49107064-49107074
18	POLR2A	chr13:49105471-49107535	GM12878	blood:	n/a	n/a
19	TAF1	chr13:49106556-49107376	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr13:49105531-49107501	GM12892	blood:	n/a	n/a
21	PML	chr13:49106222-49107444	GM12878	blood:	n/a	n/a
22	POLR2A	chr13:49105977-49107540	K562	blood:	n/a	n/a
23	POLR2A	chr13:49105070-49108079	GM15510	blood:	n/a	n/a
24	TAF1	chr13:49106838-49107310	Hela-S3	cervix:	n/a	n/a
25	MAX	chr13:49106516-49107409	H1-hESC	embryonic stem cell:	n/a	chr13:49106870-49106879 chr13:49107330-49107340
26	CTCF	chr13:49107220-49107370	GM12869	blood:	n/a	n/a
27	RAD21	chr13:49107009-49107419	SK-N-SH_RA	brain:	n/a	chr13:49107376-49107389
28	RFX5	chr13:49106711-49107298	HepG2	liver:	n/a	n/a
29	POLR2A	chr13:49106392-49107446	GM12878	blood:	n/a	n/a
30	POLR2A	chr13:49106404-49107614	MCF-7	breast:	n/a	n/a
31	POLR2A	chr13:49106547-49107319	HepG2	liver:	n/a	n/a
32	POLR2A	chr13:49104184-49108569	GM19099	blood:	n/a	n/a
33	YY1	chr13:49107132-49107281	K562	blood:	n/a	n/a
34	POLR2A	chr13:49106447-49107820	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr13:49107153-49107310	GM19238	blood:	n/a	n/a
36	POLR2A	chr13:49105884-49107692	Raji	blood:	n/a	n/a
37	POLR2A	chr13:49106409-49107614	MCF-7	breast:	n/a	n/a
38	PAX5	chr13:49107058-49107378	GM12878	blood:	n/a	n/a
39	ZEB1	chr13:49107048-49107335	GM12878	blood:	n/a	n/a
40	EBF1	chr13:49106488-49107402	GM12878	blood:	n/a	chr13:49107017-49107028
41	MAX	chr13:49106723-49107399	K562	blood:	n/a	chr13:49106870-49106879 chr13:49107330-49107340
42	REST	chr13:49106258-49107384	HL-60	blood:	n/a	n/a
43	BHLHE40	chr13:49106617-49107363	K562	blood:	n/a	n/a
44	MYC	chr13:49106461-49107245	MCF10A-Er-Src	breast:	n/a	chr13:49106870-49106879
45	TCF12	chr13:49106420-49107619	ECC-1	luminal epithelium:	n/a	n/a
46	TBP	chr13:49106128-49107272	HepG2	liver:	n/a	n/a
47	TAF1	chr13:49106313-49107405	SK-N-SH	brain:	n/a	n/a
48	TAF1	chr13:49106286-49107327	K562	blood:	n/a	n/a
49	PML	chr13:49106449-49107260	MCF-7	breast:	n/a	n/a
50	BHLHE40	chr13:49106704-49107329	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:49107002..49107509-chr13:107220001..107220517,2	Hela-S3	cervix:
2	chr13:49106818..49107420-chr2:172967559..172968104,2	HCT-116	colon:
3	chr13:31191032..31191832-chr13:49106658..49107318,2	HCT-116	colon:
4	chr13:49106639..49107516-chr14:60714929..60715777,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RB1-2	chr13:49106976-49107897	NONHSAT033718

Variant related genes	Relation type
RCBTB2	TF binding region
ENSG00000254718	Chromatin interaction
ENSG00000132952	Chromatin interaction
ENSG00000134884	Chromatin interaction
ENSG00000236651	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000189403	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs61948348	1.00[AFR][1000 genomes]
rs61948349	1.00[AFR][1000 genomes]
rs6561462	0.91[AMR][1000 genomes]
rs6561464	0.89[AMR][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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 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	chr13:49105400-49107800	Active TSS	Right Atrium	heart
2	chr13:49105600-49107600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:49105600-49107600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:49105600-49107800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
5	chr13:49105600-49107800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr13:49105800-49107400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:49105800-49107400	Active TSS	Brain Hippocampus Middle	brain
8	chr13:49105800-49107400	Active TSS	Fetal Intestine Large	intestine
9	chr13:49105800-49107400	Active TSS	Fetal Muscle Trunk	muscle
10	chr13:49105800-49107400	Active TSS	Placenta	Placenta
11	chr13:49105800-49107400	Active TSS	Psoas Muscle	Psoas
12	chr13:49105800-49107600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr13:49105800-49107600	Active TSS	Fetal Intestine Small	intestine
14	chr13:49105800-49107600	Active TSS	Left Ventricle	heart
15	chr13:49105800-49107600	Active TSS	Ovary	ovary
16	chr13:49105800-49107600	Active TSS	Pancreas	Pancrea
17	chr13:49105800-49107600	Active TSS	HSMM	muscle
18	chr13:49105800-49107800	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr13:49105800-49107800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr13:49105800-49107800	Active TSS	Aorta	Aorta
21	chr13:49105800-49107800	Active TSS	Duodenum Mucosa	Duodenum
22	chr13:49105800-49107800	Active TSS	Fetal Kidney	kidney
23	chr13:49105800-49107800	Active TSS	A549	lung
24	chr13:49105800-49108000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr13:49106000-49107400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:49106000-49107400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:49106000-49107400	Active TSS	Gastric	stomach
28	chr13:49106000-49107400	Active TSS	Lung	lung
29	chr13:49106000-49107400	Active TSS	Spleen	Spleen
30	chr13:49106000-49107600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr13:49106000-49107600	Active TSS	Colon Smooth Muscle	Colon
32	chr13:49106000-49107600	Active TSS	Esophagus	oesophagus
33	chr13:49106000-49107600	Active TSS	Small Intestine	intestine
34	chr13:49106000-49107800	Active TSS	Right Ventricle	heart
35	chr13:49106000-49108000	Active TSS	H1 Cell Line	embryonic stem cell
36	chr13:49106000-49108000	Active TSS	H9 Cell Line	embryonic stem cell
37	chr13:49106200-49107400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr13:49106200-49107400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr13:49106200-49107400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr13:49106200-49107400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr13:49106200-49107400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr13:49106200-49107400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:49106200-49107400	Active TSS	Adipose Nuclei	Adipose
44	chr13:49106200-49107400	Active TSS	Brain Angular Gyrus	brain
45	chr13:49106200-49107400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr13:49106200-49107400	Active TSS	Fetal Muscle Leg	muscle
47	chr13:49106200-49107400	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr13:49106200-49107400	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr13:49106200-49107400	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr13:49106200-49107400	Active TSS	Stomach Mucosa	stomach

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