Variant report

Variant	rs5960531
Chromosome Location	chrX:55934687-55934688
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	CTCF	chrX:55934540-55934690	HCFaa	heart:	n/a	n/a
2	CTCF	chrX:55934540-55934690	GM12867	blood:	n/a	n/a
3	EGR1	chrX:55934243-55934795	MCF-7	breast:	n/a	chrX:55934490-55934503 chrX:55934492-55934502 chrX:55934491-55934505 chrX:55934486-55934508 chrX:55934493-55934502 chrX:55934490-55934504 chrX:55934489-55934504 chrX:55934491-55934502 chrX:55934490-55934503 chrX:55934490-55934503 chrX:55934490-55934503 chrX:55934486-55934496 chrX:55934492-55934502 chrX:55934491-55934502
4	CTCF	chrX:55934540-55934690	HFF-Myc	foreskin:	n/a	n/a
5	RAD21	chrX:55934352-55934989	GM12878	blood:	n/a	n/a
6	CTCF	chrX:55934560-55934710	GM12873	blood:	n/a	n/a
7	PBX3	chrX:55934671-55934919	GM12878	blood:	n/a	n/a
8	RAD21	chrX:55934228-55934934	HCT-116	colon:	n/a	n/a
9	CTCF	chrX:55934464-55934726	Spleen_OC	spleen:	n/a	n/a
10	RAD21	chrX:55934332-55934713	GM12878	blood:	n/a	n/a
11	CTCF	chrX:55934495-55934747	T-47D	breast:	n/a	n/a
12	RAD21	chrX:55934249-55934805	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chrX:55934635-55934885	GM12892	blood:	n/a	n/a
14	CTCF	chrX:55934468-55934809	GM19239	blood:	n/a	n/a
15	CTCF	chrX:55934600-55934750	HCT-116	colon:	n/a	n/a
16	PAX5	chrX:55934450-55934701	GM12878	blood:	n/a	n/a
17	GABPA	chrX:55934329-55934829	MCF-7	breast:	n/a	n/a
18	ZNF143	chrX:55934382-55935704	GM12878	blood:	n/a	n/a
19	CTCF	chrX:55934580-55934730	GM12875	blood:	n/a	n/a
20	POLR2A	chrX:55934220-55936344	GM12891	blood:	n/a	n/a
21	MAX	chrX:55934335-55934984	GM12878	blood:	n/a	chrX:55934492-55934501
22	CTCF	chrX:55934560-55934710	AG10803	skin:	n/a	n/a
23	EGR1	chrX:55934211-55934879	HCT-116	colon:	n/a	chrX:55934490-55934503 chrX:55934492-55934502 chrX:55934491-55934505 chrX:55934486-55934508 chrX:55934493-55934502 chrX:55934490-55934504 chrX:55934489-55934504 chrX:55934491-55934502 chrX:55934490-55934503 chrX:55934490-55934503 chrX:55934490-55934503 chrX:55934486-55934496 chrX:55934492-55934502 chrX:55934491-55934502
24	ELF1	chrX:55934386-55934876	MCF-7	breast:	n/a	n/a
25	CTCF	chrX:55934530-55934696	GM20000	blood:	n/a	n/a
26	EGR1	chrX:55934337-55934714	ECC-1	luminal epithelium:	n/a	chrX:55934490-55934503 chrX:55934492-55934502 chrX:55934491-55934505 chrX:55934486-55934508 chrX:55934493-55934502 chrX:55934490-55934504 chrX:55934489-55934504 chrX:55934491-55934502 chrX:55934490-55934503 chrX:55934490-55934503 chrX:55934490-55934503 chrX:55934486-55934496 chrX:55934492-55934502 chrX:55934491-55934502
27	YY1	chrX:55934407-55934813	GM12892	blood:	n/a	chrX:55934492-55934506
28	CTCF	chrX:55934540-55934690	HMF	breast:	n/a	n/a
29	POLR2A	chrX:55934667-55934907	GM12891	blood:	n/a	n/a
30	GATA1	chrX:55934485-55935564	PBDE	blood:	n/a	chrX:55935534-55935543
31	ZNF217	chrX:55934507-55934824	MCF-7	breast:	n/a	n/a
32	POLR2A	chrX:55934323-55935696	GM15510	blood:	n/a	n/a
33	CTCF	chrX:55934560-55934710	AG09319	gingival:	n/a	n/a
34	CTCF	chrX:55934346-55934883	MCF-7	breast:	n/a	n/a
35	CTCF	chrX:55934660-55934810	WI-38	lung:	n/a	n/a
36	POLR2A	chrX:55934127-55936922	GM12878	blood:	n/a	n/a
37	NFIC	chrX:55934346-55935025	GM12878	blood:	n/a	n/a
38	WRNIP1	chrX:55934349-55934911	GM12878	blood:	n/a	n/a
39	RCOR1	chrX:55934362-55935665	GM12878	blood:	n/a	n/a
40	CTCF	chrX:55934447-55934761	Pancreas_OC	pancreas:	n/a	n/a
41	EGR1	chrX:55934268-55934781	ECC-1	luminal epithelium:	n/a	chrX:55934490-55934503 chrX:55934492-55934502 chrX:55934491-55934505 chrX:55934486-55934508 chrX:55934493-55934502 chrX:55934490-55934504 chrX:55934489-55934504 chrX:55934491-55934502 chrX:55934490-55934503 chrX:55934490-55934503 chrX:55934490-55934503 chrX:55934486-55934496 chrX:55934492-55934502 chrX:55934491-55934502
42	CTCF	chrX:55934580-55934730	HEEpiC	esophagus:	n/a	n/a
43	CTCF	chrX:55934540-55934690	RPTEC	kidney:	n/a	n/a
44	ELF1	chrX:55934343-55934748	GM12878	blood:	n/a	n/a
45	RCOR1	chrX:55934568-55934784	K562	blood:	n/a	n/a
46	CTCF	chrX:55934560-55934710	GM12869	blood:	n/a	n/a
47	RAD21	chrX:55934403-55934774	SK-N-SH_RA	brain:	n/a	n/a
48	CTCF	chrX:55934580-55934730	AG09309	skin:	n/a	n/a
49	CTCF	chrX:55934560-55934710	GM12875	blood:	n/a	n/a
50	CTCF	chrX:55934523-55934747	ProgFib	skin:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrX:55934670-55934720	H1-hESC	embryonic stem cell:	embryo
2	chrX:55934670-55934720	HEEpiC	esophagus:	n/a
3	chrX:55934670-55934720	HCT-116	colon:	n/a
4	chrX:55934670-55934720	MCF-7	breast:	n/a
5	chrX:55934670-55934720	Hela-S3	cervix:	n/a
6	chrX:55934670-55934720	NHBE	bronchial:	n/a
7	chrX:55934670-55934720	HNPCEpiC	eye:	n/a
8	chrX:55934670-55934720	CMK	blood:	n/a
9	chrX:55934670-55934720	GM19239	blood:	n/a
10	chrX:55934670-55934720	HRPEpiC	eye:	n/a
11	chrX:55934670-55934720	ProgFib	skin:	n/a
12	chrX:55934670-55934720	GM12892	blood:	n/a
13	chrX:55934670-55934720	LNCaP	prostate:	n/a
14	chrX:55934670-55934720	Jurkat	blood:	n/a
15	chrX:55934670-55934720	AoSMC	blood vessel:	n/a
16	chrX:55934670-55934720	SAEC	small airway:	n/a
17	chrX:55934670-55934720	AG04449	skin:	fetal
18	chrX:55934670-55934720	HCM	heart:	n/a
19	chrX:55934670-55934720	HMEC	breast:	n/a
20	chrX:55934670-55934720	HAEpiC	amniotic membrane:	n/a
21	chrX:55934670-55934720	HPAEpiC	pulmonary alveolar:	n/a
22	chrX:55934670-55934720	NH-A	brain:	n/a
23	chrX:55934670-55934720	GM12878	blood:	n/a
24	chrX:55934670-55934720	HEK293	kidney:	embryo
25	chrX:55934670-55934720	SK-N-SH_RA	brain:	n/a
26	chrX:55934670-55934720	SKMC	muscle:	n/a
27	chrX:55934670-55934720	GM06990	blood:	n/a
28	chrX:55934670-55934720	AG10803	skin:	n/a
29	chrX:55934670-55934720	HRCEpiC	kidney:	n/a
30	chrX:55934670-55934720	ovcar-3	ovarian:	n/a
31	chrX:55934670-55934720	PANC-1	pancreas:	n/a
32	chrX:55934670-55934720	U87	brain:	n/a
33	chrX:55934670-55934720	RPTEC	kidney:	n/a
34	chrX:55934670-55934720	T-47D	breast:	n/a
35	chrX:55934670-55934720	BE2_C	brain:	n/a
36	chrX:55934670-55934720	Hepatocyte	liver:	n/a
37	chrX:55934670-55934720	HRE	kidney:	n/a
38	chrX:55934670-55934720	AG09309	skin:	n/a
39	chrX:55934670-55934720	HIPEpiC	eye:	n/a
40	chrX:55934670-55934720	K562	blood:	n/a
41	chrX:55934670-55934720	GM12891	blood:	n/a
42	chrX:55934670-55934720	PrEC	prostate:	n/a
43	chrX:55934670-55934720	HepG2	liver:	n/a
44	chrX:55934670-55934720	A549	lung:	n/a
45	chrX:55934670-55934720	HUVEC	blood vessel:	n/a
46	chrX:55934670-55934720	NB4	blood:	n/a
47	chrX:55934670-55934720	Caco-2	colon:	n/a
48	chrX:55934670-55934720	HCF	heart:	n/a
49	chrX:55934670-55934720	AG04450	lung:	fetal
50	chrX:55934670-55934720	PFSK-1	brain:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL353698.1-2	chrX:55934556-55935233	ENSG00000227486.1

Variant related genes	Relation type
ENSG00000252961	TF binding region
ENSG00000252961	CpG island

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3384643	chrX:55919980-55939813	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
2	esv2752678	chrX:55930768-56851953	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2753382	chrX:55930768-56851953	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2754448	chrX:55930768-56851953	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2755974	chrX:55930768-56851953	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv432333	chrX:55930768-56851953	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:55933600-55936400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chrX:55933600-55939000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chrX:55933800-55936200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chrX:55934000-55936000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chrX:55934000-55936000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chrX:55934000-55936000	Active TSS	Rectal Smooth Muscle	rectum
7	chrX:55934000-55938800	Active TSS	GM12878-XiMat	blood
8	chrX:55934200-55934800	Active TSS	Primary hematopoietic stem cells	blood
9	chrX:55934200-55935600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chrX:55934200-55935600	Active TSS	Colon Smooth Muscle	Colon
11	chrX:55934200-55935600	Active TSS	Fetal Brain Male	brain
12	chrX:55934200-55935800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chrX:55934200-55935800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chrX:55934200-55935800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
15	chrX:55934200-55935800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chrX:55934200-55935800	Active TSS	Brain Angular Gyrus	brain
17	chrX:55934200-55935800	Active TSS	Brain Hippocampus Middle	brain
18	chrX:55934200-55935800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
19	chrX:55934200-55935800	Active TSS	HSMM	muscle
20	chrX:55934200-55935800	Active TSS	Monocytes-CD14+_RO01746	blood
21	chrX:55934200-55936000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chrX:55934200-55936000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chrX:55934200-55936000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chrX:55934200-55936000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chrX:55934200-55936000	Active TSS	Brain Anterior Caudate	brain
26	chrX:55934200-55936000	Active TSS	Colonic Mucosa	Colon
27	chrX:55934200-55936200	Active TSS	Duodenum Mucosa	Duodenum
28	chrX:55934200-55936200	Bivalent/Poised TSS	Fetal Brain Female	brain
29	chrX:55934200-55936200	Active TSS	Rectal Mucosa Donor 29	rectum
30	chrX:55934200-55936400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chrX:55934200-55936400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
32	chrX:55934200-55936400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chrX:55934400-55934800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chrX:55934400-55934800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chrX:55934400-55934800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chrX:55934400-55934800	Enhancers	Spleen	Spleen
37	chrX:55934400-55935000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chrX:55934400-55935200	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chrX:55934400-55935400	Bivalent/Poised TSS	Fetal Stomach	stomach
40	chrX:55934400-55935600	Active TSS	Primary monocytes fromperipheralblood	blood
41	chrX:55934400-55935600	Active TSS	Adipose Nuclei	Adipose
42	chrX:55934400-55935600	Active TSS	Placenta	Placenta
43	chrX:55934400-55935600	Active TSS	Left Ventricle	heart
44	chrX:55934400-55935800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chrX:55934400-55935800	Active TSS	H1 Cell Line	embryonic stem cell
46	chrX:55934400-55935800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chrX:55934400-55935800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chrX:55934400-55935800	Active TSS	Primary T helper cells fromperipheralblood	blood
49	chrX:55934400-55935800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chrX:55934400-55935800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links