Variant report

Variant	rs1199961
Chromosome Location	chr13:37634151-37634152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:98)
CpG islands
(count:122)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:98 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:37632937-37634197	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr13:37632182-37634327	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr13:37633293-37634210	ProgFib	skin:	n/a	n/a
4	ELF1	chr13:37633173-37634151	MCF-7	breast:	n/a	n/a
5	MAZ	chr13:37632688-37634232	GM12878	blood:	n/a	chr13:37633160-37633169 chr13:37633876-37633886
6	POLR2A	chr13:37632590-37634213	GM18505	blood:	n/a	n/a
7	HCFC1	chr13:37633221-37634274	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr13:37633473-37634232	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr13:37633522-37634172	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr13:37633021-37634210	GM19193	blood:	n/a	n/a
11	MAX	chr13:37633181-37634189	A549	lung:	n/a	chr13:37633876-37633886
12	POLR2A	chr13:37632407-37634154	MCF10A-Er-Src	breast:	n/a	n/a
13	GABPA	chr13:37633374-37634156	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr13:37632647-37634224	GM12878	blood:	n/a	n/a
15	POLR2A	chr13:37633570-37634178	HCT-116	colon:	n/a	n/a
16	SIN3AK20	chr13:37632938-37634285	MCF-7	breast:	n/a	n/a
17	POLR2A	chr13:37633291-37634332	U87	brain:	n/a	n/a
18	TAF1	chr13:37633242-37634201	ECC-1	luminal epithelium:	n/a	n/a
19	GABPA	chr13:37633487-37634167	HL-60	blood:	n/a	n/a
20	POLR2A	chr13:37632993-37634248	HUVEC	blood vessel:	n/a	n/a
21	ELK1	chr13:37633458-37634188	GM12878	blood:	n/a	n/a
22	MAX	chr13:37632969-37634171	NB4	blood:	n/a	chr13:37633160-37633169 chr13:37633876-37633886
23	POLR2A	chr13:37633255-37634252	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr13:37633369-37634225	GM12878	blood:	n/a	n/a
25	POLR2A	chr13:37633511-37634178	HEK293	kidney:	n/a	n/a
26	POLR2A	chr13:37633491-37634181	HepG2	liver:	n/a	n/a
27	POLR2A	chr13:37633152-37634192	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr13:37633088-37634151	GM15510	blood:	n/a	n/a
29	POLR2A	chr13:37633318-37634534	HepG2	liver:	n/a	n/a
30	POLR2A	chr13:37632749-37634155	HepG2	liver:	n/a	n/a
31	RCOR1	chr13:37633954-37634172	K562	blood:	n/a	n/a
32	NFIC	chr13:37633567-37634173	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr13:37633091-37634219	GM18951	blood:	n/a	n/a
34	POLR2A	chr13:37632901-37634201	PBDE	blood:	n/a	n/a
35	POLR2A	chr13:37633187-37634180	GM18526	blood:	n/a	n/a
36	TBL1XR1	chr13:37633525-37634181	GM12878	blood:	n/a	n/a
37	POLR2A	chr13:37633019-37634177	MCF-7	breast:	n/a	n/a
38	EP300	chr13:37633436-37634211	SK-N-SH	brain:	n/a	n/a
39	SP1	chr13:37633520-37634205	A549	lung:	n/a	chr13:37633836-37633850 chr13:37633877-37633886 chr13:37633875-37633886 chr13:37633841-37633850 chr13:37633875-37633887 chr13:37633961-37633970 chr13:37633876-37633885 chr13:37633841-37633850 chr13:37633876-37633886 chr13:37633861-37633873 chr13:37633959-37633971 chr13:37633959-37633971 chr13:37633959-37633970 chr13:37633875-37633887 chr13:37633956-37633970 chr13:37633960-37633969 chr13:37633872-37633886 chr13:37633840-37633849
40	CEBPB	chr13:37633197-37634154	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr13:37633041-37634151	K562	blood:	n/a	n/a
42	TAF1	chr13:37633028-37634151	H1-hESC	embryonic stem cell:	n/a	n/a
43	RUNX3	chr13:37633100-37634157	GM12878	blood:	n/a	n/a
44	POLR2A	chr13:37632359-37634223	GM12878	blood:	n/a	n/a
45	PML	chr13:37632962-37634230	GM12878	blood:	n/a	n/a
46	POLR2A	chr13:37633420-37634189	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr13:37634040-37634190	AG10803	skin:	n/a	n/a
48	CHD2	chr13:37633442-37634163	GM12878	blood:	n/a	chr13:37633956-37633966
49	MAZ	chr13:37632768-37634282	IMR90	lung:	n/a	chr13:37633160-37633169 chr13:37633876-37633886
50	POLR2A	chr13:37632477-37634230	MCF10A-Er-Src	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:37634133-37634183	PFSK-1	brain:	n/a
2	chr13:37634133-37634183	LNCaP	prostate:	n/a
3	chr13:37634127-37634177	MCF10A-Er-Src	breast:	n/a
4	chr13:37634127-37634177	HEK293	kidney:	embryo
5	chr13:37634133-37634183	GM19239	blood:	n/a
6	chr13:37634127-37634177	HRE	kidney:	n/a
7	chr13:37634127-37634177	Hepatocyte	liver:	n/a
8	chr13:37634133-37634183	GM12878	blood:	n/a
9	chr13:37634133-37634183	SK-N-SH	brain:	n/a
10	chr13:37634127-37634177	GM12892	blood:	n/a
11	chr13:37634133-37634183	HUVEC	blood vessel:	n/a
12	chr13:37634127-37634177	CMK	blood:	n/a
13	chr13:37634127-37634177	AG09319	gingival:	n/a
14	chr13:37634133-37634183	HAEpiC	amniotic membrane:	n/a
15	chr13:37634127-37634177	HCM	heart:	n/a
16	chr13:37634127-37634177	U87	brain:	n/a
17	chr13:37634127-37634177	Jurkat	blood:	n/a
18	chr13:37634127-37634177	BE2_C	brain:	n/a
19	chr13:37634133-37634183	HCT-116	colon:	n/a
20	chr13:37634133-37634183	Jurkat	blood:	n/a
21	chr13:37634127-37634177	ProgFib	skin:	n/a
22	chr13:37634127-37634177	HCT-116	colon:	n/a
23	chr13:37634127-37634177	T-47D	breast:	n/a
24	chr13:37634133-37634183	NHBE	bronchial:	n/a
25	chr13:37634127-37634177	AG04449	skin:	fetal
26	chr13:37634133-37634183	MCF10A-Er-Src	breast:	n/a
27	chr13:37634127-37634177	SAEC	small airway:	n/a
28	chr13:37634133-37634183	Hela-S3	cervix:	n/a
29	chr13:37634127-37634177	MCF-7	breast:	n/a
30	chr13:37634127-37634177	HL-60	blood:	n/a
31	chr13:37634127-37634177	IMR90	lung:	fetal
32	chr13:37634133-37634183	BE2_C	brain:	n/a
33	chr13:37634133-37634183	Caco-2	colon:	n/a
34	chr13:37634133-37634183	NH-A	brain:	n/a
35	chr13:37634127-37634177	SKMC	muscle:	n/a
36	chr13:37634127-37634177	GM12878	blood:	n/a
37	chr13:37634127-37634177	SK-N-SH_RA	brain:	n/a
38	chr13:37634127-37634177	RPTEC	kidney:	n/a
39	chr13:37634133-37634183	GM12892	blood:	n/a
40	chr13:37634127-37634177	HCPEpiC	choroid plexus:	n/a
41	chr13:37634133-37634183	CMK	blood:	n/a
42	chr13:37634127-37634177	HPAEpiC	pulmonary alveolar:	n/a
43	chr13:37634133-37634183	K562	blood:	n/a
44	chr13:37634127-37634177	SK-N-MC	brain:	n/a
45	chr13:37634127-37634177	HNPCEpiC	eye:	n/a
46	chr13:37634127-37634177	AG04450	lung:	fetal
47	chr13:37634133-37634183	AG04450	lung:	fetal
48	chr13:37634127-37634177	HepG2	liver:	n/a
49	chr13:37634133-37634183	ECC-1	luminal epithelium:	n/a
50	chr13:37634133-37634183	GM06990	blood:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:37633556..37634211-chr15:41708713..41709407,2	HCT-116	colon:
2	chr13:37573339..37577948-chr13:37631578..37635345,7	K562	blood:
3	chr13:37572711..37577948-chr13:37631792..37635345,6	K562	blood:
4	chr13:37631915..37634175-chr16:87992203..87994742,2	MCF-7	breast:
5	chr13:37573411..37578166-chr13:37631570..37635674,7	MCF-7	breast:
6	chr13:37634022..37636359-chr13:37636430..37638160,2	MCF-7	breast:
7	chr13:37572134..37576910-chr13:37632372..37635841,8	MCF-7	breast:

No data

Variant related genes	Relation type
SUPT20H	TF binding region
SUPT20H	CpG island
ENSG00000172530	Chromatin interaction
ENSG00000137815	Chromatin interaction
ENSG00000120697	Chromatin interaction
ENSG00000120699	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1199957	0.82[ASW][hapmap];0.84[LWK][hapmap];0.81[AFR][1000 genomes]
rs1199965	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1199971	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1208131	0.83[AFR][1000 genomes]
rs1627791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17054770	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs1764485	0.81[AFR][1000 genomes]
rs2485063	0.81[AFR][1000 genomes]
rs2670058	0.90[ASW][hapmap]
rs57549356	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3377840	chr13:37631001-37656330	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	5 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	chr13:37631600-37634600	Active TSS	HSMM	muscle
2	chr13:37631600-37634800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:37631800-37634600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:37631800-37634600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr13:37632000-37634600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr13:37632200-37634200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr13:37632200-37634200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr13:37632200-37634200	Active TSS	NHLF	lung
9	chr13:37632200-37634400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr13:37632200-37634400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr13:37632200-37634400	Active TSS	Fetal Intestine Small	intestine
12	chr13:37632200-37634400	Active TSS	Stomach Smooth Muscle	stomach
13	chr13:37632200-37634400	Active TSS	A549	lung
14	chr13:37632200-37634600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:37632200-37634600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr13:37632200-37634600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr13:37632200-37634600	Active TSS	Colonic Mucosa	Colon
18	chr13:37632200-37634800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr13:37632400-37634200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:37632400-37634200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr13:37632400-37634200	Active TSS	NHDF-Ad	bronchial
22	chr13:37632400-37634400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr13:37632400-37634400	Active TSS	Fetal Brain Male	brain
24	chr13:37632400-37634400	Active TSS	Fetal Intestine Large	intestine
25	chr13:37632400-37634400	Active TSS	Right Atrium	heart
26	chr13:37632400-37634400	Active TSS	Stomach Mucosa	stomach
27	chr13:37632400-37634400	Active TSS	HSMMtube	muscle
28	chr13:37632400-37634400	Active TSS	Osteobl	bone
29	chr13:37632400-37634600	Active TSS	Muscle Satellite Cultured Cells	--
30	chr13:37632400-37634600	Active TSS	K562	blood
31	chr13:37632400-37634800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr13:37632400-37635000	Active TSS	Fetal Kidney	kidney
33	chr13:37632600-37634200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr13:37632600-37634200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr13:37632600-37634200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr13:37632600-37634200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr13:37632600-37634200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:37632600-37634200	Active TSS	Fetal Thymus	thymus
39	chr13:37632600-37634400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr13:37632600-37634400	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr13:37632600-37634400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:37632600-37634400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr13:37632600-37634400	Active TSS	Fetal Muscle Leg	muscle
44	chr13:37632600-37634600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr13:37632600-37634600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:37632600-37634600	Active TSS	Right Ventricle	heart
47	chr13:37632800-37634200	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr13:37632800-37634200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr13:37632800-37634200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr13:37632800-37634200	Active TSS	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links