Variant report

Variant	rs61908739
Chromosome Location	chr11:100557985-100557986
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	UBTF	chr11:100557668-100558873	K562	blood:	n/a	n/a
2	POLR2A	chr11:100557644-100558480	A549	lung:	n/a	n/a
3	GABPA	chr11:100557907-100558264	GM12878	blood:	n/a	chr11:100558188-100558197 chr11:100558195-100558206 chr11:100558192-100558206
4	RCOR1	chr11:100557879-100558860	K562	blood:	n/a	n/a
5	POLR2A	chr11:100557778-100558263	MCF-7	breast:	n/a	n/a
6	MAX	chr11:100557648-100558999	HCT-116	colon:	n/a	n/a
7	ZNF263	chr11:100557279-100558877	HEK293-T-REx	kidney:	n/a	chr11:100558219-100558228
8	POLR2A	chr11:100557227-100558736	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr11:100557860-100558010	WERI-Rb-1	eye:	n/a	n/a
10	MAX	chr11:100557943-100558224	K562	blood:	n/a	n/a
11	CHD2	chr11:100557688-100558771	GM12878	blood:	n/a	n/a
12	EGR1	chr11:100557491-100559434	HCT-116	colon:	n/a	chr11:100558120-100558133 chr11:100558121-100558132 chr11:100558121-100558130 chr11:100559151-100559162 chr11:100558117-100558131 chr11:100558120-100558133 chr11:100558121-100558131 chr11:100558059-100558068 chr11:100558119-100558133 chr11:100557788-100557797 chr11:100558120-100558133 chr11:100558196-100558205 chr11:100557640-100557655 chr11:100558120-100558130
13	RCOR1	chr11:100557975-100558217	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:100557857-100558125	HUVEC	blood vessel:	n/a	n/a
15	SIN3AK20	chr11:100557892-100558201	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr11:100557851-100558916	GM12878	blood:	n/a	chr11:100558695-100558704
17	POLR2A	chr11:100557825-100558769	GM18951	blood:	n/a	n/a
18	POLR2A	chr11:100557626-100558825	HepG2	liver:	n/a	n/a
19	NRF1	chr11:100557656-100558262	H1-hESC	embryonic stem cell:	n/a	chr11:100558188-100558197 chr11:100558195-100558206 chr11:100557787-100557798 chr11:100558192-100558206
20	GABPA	chr11:100557880-100558319	A549	lung:	n/a	chr11:100558188-100558197 chr11:100558195-100558206 chr11:100558192-100558206
21	BRCA1	chr11:100557962-100558162	GM12878	blood:	n/a	n/a
22	EBF1	chr11:100557871-100558250	GM12878	blood:	n/a	n/a
23	EGR1	chr11:100557870-100558328	H1-hESC	embryonic stem cell:	n/a	chr11:100558120-100558133 chr11:100558121-100558132 chr11:100558121-100558130 chr11:100558117-100558131 chr11:100558120-100558133 chr11:100558121-100558131 chr11:100558059-100558068 chr11:100558119-100558133 chr11:100558120-100558133 chr11:100558196-100558205 chr11:100558120-100558130
24	POLR2A	chr11:100557839-100558377	HUVEC	blood vessel:	n/a	n/a
25	GABPA	chr11:100557974-100558204	HepG2	liver:	n/a	chr11:100558188-100558197
26	BACH1	chr11:100557257-100558831	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr11:100557821-100558381	GM12878	blood:	n/a	n/a
28	POLR2A	chr11:100557698-100558271	K562	blood:	n/a	n/a
29	ZBTB7A	chr11:100557805-100558333	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr11:100557786-100558809	HCT-116	colon:	n/a	n/a
31	ELF1	chr11:100557940-100558150	HepG2	liver:	n/a	chr11:100558058-100558067 chr11:100558097-100558109 chr11:100558055-100558068
32	GABPA	chr11:100557954-100558183	GM12878	blood:	n/a	n/a
33	HEY1	chr11:100557880-100558293	K562	blood:	n/a	chr11:100558250-100558265 chr11:100558185-100558200 chr11:100558248-100558263 chr11:100558234-100558249 chr11:100558241-100558256
34	MAX	chr11:100557850-100558890	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr11:100557889-100558864	MCF10A-Er-Src	breast:	n/a	n/a
36	CTCF	chr11:100557840-100557990	GM12871	blood:	n/a	n/a
37	CHD1	chr11:100557858-100558760	GM12878	blood:	n/a	n/a
38	TAF1	chr11:100557735-100558129	K562	blood:	n/a	n/a
39	BCLAF1	chr11:100557816-100558326	GM12878	blood:	n/a	chr11:100557970-100557979 chr11:100558059-100558068 chr11:100558094-100558107 chr11:100558097-100558110 chr11:100558181-100558194
40	TAF7	chr11:100557657-100558222	H1-hESC	embryonic stem cell:	n/a	n/a
41	E2F6	chr11:100557886-100558292	K562	blood:	n/a	chr11:100558241-100558251 chr11:100558196-100558205 chr11:100558120-100558130 chr11:100558185-100558194 chr11:100558244-100558253
42	POLR2A	chr11:100557768-100558758	GM12892	blood:	n/a	n/a
43	POLR2A	chr11:100557859-100558092	HepG2	liver:	n/a	n/a
44	MXI1	chr11:100557864-100558855	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr11:100557967-100559339	MCF10A-Er-Src	breast:	n/a	n/a
46	CTCF	chr11:100557900-100558050	HUVEC	blood vessel:	n/a	n/a
47	MAX	chr11:100557914-100558781	GM12878	blood:	n/a	n/a
48	MAX	chr11:100557609-100558410	HepG2	liver:	n/a	n/a
49	PAX5	chr11:100557795-100558442	GM12892	blood:	n/a	n/a
50	MAX	chr11:100557894-100558907	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:100557958-100558008	HCM	heart:	n/a
2	chr11:100557954-100558004	ovcar-3	ovarian:	n/a
3	chr11:100557954-100558004	K562	blood:	n/a
4	chr11:100557958-100558008	LNCaP	prostate:	n/a
5	chr11:100557958-100558008	MCF-7	breast:	n/a
6	chr11:100557954-100558004	ECC-1	luminal epithelium:	n/a
7	chr11:100557958-100558008	SK-N-SH	brain:	n/a
8	chr11:100557958-100558008	H1-hESC	embryonic stem cell:	embryo
9	chr11:100557958-100558008	AG04449	skin:	fetal
10	chr11:100557958-100558008	SKMC	muscle:	n/a
11	chr11:100557954-100558004	U87	brain:	n/a
12	chr11:100557958-100558008	A549	lung:	n/a
13	chr11:100557958-100558008	HEK293	kidney:	embryo
14	chr11:100557954-100558004	MCF10A-Er-Src	breast:	n/a
15	chr11:100557954-100558004	SK-N-SH	brain:	n/a
16	chr11:100557954-100558004	Hela-S3	cervix:	n/a
17	chr11:100557958-100558008	GM06990	blood:	n/a
18	chr11:100557954-100558004	A549	lung:	n/a
19	chr11:100557954-100558004	AG04450	lung:	fetal
20	chr11:100557954-100558004	HCPEpiC	choroid plexus:	n/a
21	chr11:100557958-100558008	AoSMC	blood vessel:	n/a
22	chr11:100557958-100558008	HMEC	breast:	n/a
23	chr11:100557958-100558008	AG09319	gingival:	n/a
24	chr11:100557954-100558004	HepG2	liver:	n/a
25	chr11:100557954-100558004	AG04449	skin:	fetal
26	chr11:100557958-100558008	ECC-1	luminal epithelium:	n/a
27	chr11:100557958-100558008	NH-A	brain:	n/a
28	chr11:100557958-100558008	NT2-D1	testis:	n/a
29	chr11:100557958-100558008	HIPEpiC	eye:	n/a
30	chr11:100557958-100558008	PANC-1	pancreas:	n/a
31	chr11:100557958-100558008	HRE	kidney:	n/a
32	chr11:100557958-100558008	U87	brain:	n/a
33	chr11:100557954-100558004	NHBE	bronchial:	n/a
34	chr11:100557958-100558008	GM12891	blood:	n/a
35	chr11:100557954-100558004	MCF-7	breast:	n/a
36	chr11:100557958-100558008	IMR90	lung:	fetal
37	chr11:100557954-100558004	HCF	heart:	n/a
38	chr11:100557958-100558008	HepG2	liver:	n/a
39	chr11:100557958-100558008	HRCEpiC	kidney:	n/a
40	chr11:100557958-100558008	PrEC	prostate:	n/a
41	chr11:100557958-100558008	Hepatocyte	liver:	n/a
42	chr11:100557958-100558008	GM12892	blood:	n/a
43	chr11:100557954-100558004	HAEpiC	amniotic membrane:	n/a
44	chr11:100557958-100558008	HL-60	blood:	n/a
45	chr11:100557958-100558008	ovcar-3	ovarian:	n/a
46	chr11:100557958-100558008	HNPCEpiC	eye:	n/a
47	chr11:100557954-100558004	PANC-1	pancreas:	n/a
48	chr11:100557954-100558004	AG09309	skin:	n/a
49	chr11:100557954-100558004	AG10803	skin:	n/a
50	chr11:100557954-100558004	HPAEpiC	pulmonary alveolar:	n/a

Variant related genes	Relation type
ARHGAP42	TF binding region
ARHGAP42	CpG island

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17712139	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4754694	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57637131	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61472500	0.89[ASN][1000 genomes]
rs61621482	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61908735	0.83[ASN][1000 genomes]
rs61908736	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61908737	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61908738	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61908740	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61908741	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61908742	0.94[ASN][1000 genomes]
rs61908744	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61908745	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6590806	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129917	0.82[AFR][1000 genomes]
rs73001993	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053430	chr11:99888390-100629136	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1042067	chr11:99889697-100629136	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv556122	chr11:99893282-100585889	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1037689	chr11:99895378-100624599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1040942	chr11:99895378-100629136	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1039852	chr11:99901695-100610533	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv541152	chr11:99901695-100610533	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1045190	chr11:99913193-100627395	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv541153	chr11:99913193-100627395	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv529454	chr11:99913394-100627255	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1043022	chr11:100387466-100610533	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv832246	chr11:100426725-100606957	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100556600-100558000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:100557000-100560000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr11:100557200-100559000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:100557200-100559600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr11:100557200-100559600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr11:100557200-100559600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr11:100557200-100559600	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr11:100557200-100559800	Active TSS	Fetal Kidney	kidney
9	chr11:100557200-100560600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:100557400-100558600	Active TSS	Primary T cells from cord blood	blood
11	chr11:100557400-100558800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:100557400-100558800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr11:100557400-100558800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:100557400-100558800	Active TSS	Osteobl	bone
15	chr11:100557400-100559000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:100557400-100559000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:100557400-100559000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr11:100557400-100559000	Active TSS	Brain Cingulate Gyrus	brain
19	chr11:100557400-100559000	Active TSS	Rectal Smooth Muscle	rectum
20	chr11:100557400-100559000	Active TSS	Hela-S3	cervix
21	chr11:100557400-100559200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:100557400-100559200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:100557400-100559200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:100557400-100559400	Active TSS	Fetal Intestine Large	intestine
25	chr11:100557400-100559600	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr11:100557400-100559600	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr11:100557400-100559600	Active TSS	Duodenum Mucosa	Duodenum
28	chr11:100557400-100559800	Active TSS	HSMM	muscle
29	chr11:100557400-100560200	Active TSS	Brain Anterior Caudate	brain
30	chr11:100557400-100560200	Active TSS	Right Atrium	heart
31	chr11:100557400-100560600	Active TSS	Fetal Muscle Trunk	muscle
32	chr11:100557400-100561000	Active TSS	HSMMtube	muscle
33	chr11:100557600-100558000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
34	chr11:100557600-100558000	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr11:100557600-100558000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr11:100557600-100558000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:100557600-100558000	Active TSS	Brain Germinal Matrix	brain
38	chr11:100557600-100558000	Bivalent/Poised TSS	Thymus	Thymus
39	chr11:100557600-100558400	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
40	chr11:100557600-100558600	Active TSS	HUVEC	blood vessel
41	chr11:100557600-100558800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:100557600-100558800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:100557600-100558800	Active TSS	Liver	Liver
44	chr11:100557600-100558800	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr11:100557600-100558800	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
46	chr11:100557600-100559000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:100557600-100559000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:100557600-100559000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:100557600-100559000	Active TSS	Colon Smooth Muscle	Colon
50	chr11:100557600-100559000	Active TSS	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links