Variant report

Variant	rs39501
Chromosome Location	chr8:90772766-90772767
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	JUN	chr8:90771040-90772820	K562	blood:	n/a	chr8:90771657-90771666 chr8:90772350-90772361
2	TEAD4	chr8:90771967-90772776	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr8:90771960-90772877	SK-N-SH	brain:	n/a	chr8:90772350-90772361
4	EP300	chr8:90771900-90772865	SK-N-SH	brain:	n/a	chr8:90772427-90772437
5	TEAD4	chr8:90771451-90772799	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr8:90771984-90772903	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr8:90771351-90772822	SK-N-SH	brain:	n/a	chr8:90772298-90772307
8	PBX3	chr8:90771406-90772817	SK-N-SH	brain:	n/a	chr8:90771658-90771667
9	JUND	chr8:90771322-90772871	SK-N-SH	brain:	n/a	chr8:90771657-90771666 chr8:90772570-90772581 chr8:90772350-90772361
10	JUND	chr8:90771966-90772856	SK-N-SH	brain:	n/a	chr8:90772570-90772581 chr8:90772350-90772361
11	GATA3	chr8:90771237-90772945	SK-N-SH	brain:	n/a	chr8:90772298-90772307
12	TCF12	chr8:90771311-90772902	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:90770120..90773332-chr8:90778069..90782721,6	K562	blood:
2	chr8:90766360..90773428-chr8:90991217..91000142,22	MCF-7	breast:
3	chr8:90770153..90772840-chr8:91007393..91009503,2	K562	blood:
4	chr6:27099899..27102052-chr8:90770515..90773024,2	MCF-7	breast:
5	chr8:90731255..90734229-chr8:90770926..90773381,2	MCF-7	breast:
6	chr8:90735927..90738609-chr8:90772144..90774444,2	K562	blood:
7	chr8:90734885..90744209-chr8:90767977..90774247,14	MCF-7	breast:
8	chr8:90767236..90773457-chr8:90912212..90919638,16	MCF-7	breast:
9	chr8:90736815..90743993-chr8:90765696..90773918,18	MCF-7	breast:
10	chr8:90772003..90774182-chr8:90878976..90880598,2	K562	blood:
11	chr8:90766719..90773256-chr8:90991979..90999179,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251136	TF binding region
ENSG00000207359	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000164823	Chromatin interaction
ENSG00000251136	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000104320	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12156013	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13254219	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13274635	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs218935	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs218938	0.89[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs369771	0.80[CEU][hapmap]
rs383592	0.82[CEU][hapmap]
rs394108	0.80[CEU][hapmap]
rs39502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39508	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs39509	0.80[CEU][hapmap]
rs39511	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs39512	0.86[EUR][1000 genomes]
rs39515	0.80[CEU][hapmap]
rs397540	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs39762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39763	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs39766	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs398701	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40248	0.83[EUR][1000 genomes]
rs40378	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40379	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40380	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs40454	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs40635	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs406680	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs411310	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs416324	0.82[CEU][hapmap]
rs42343	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs42479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42480	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs425721	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs426779	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs428484	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs43133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434264	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs450332	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs51331	0.80[CEU][hapmap]
rs7815039	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv891181	chr8:90737258-90819998	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90770800-90773800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:90771000-90772800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr8:90771000-90773600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr8:90771000-90774200	Weak transcription	Gastric	stomach
5	chr8:90771000-90797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:90771400-90773000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr8:90771600-90773000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr8:90771600-90773000	Flanking Active TSS	Osteobl	bone
9	chr8:90771600-90774200	Enhancers	Fetal Heart	heart
10	chr8:90771600-90803800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr8:90771800-90773000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:90771800-90773200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr8:90771800-90773800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:90771800-90774200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr8:90771800-90774200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr8:90771800-90777400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:90771800-90784400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr8:90771800-90805000	Weak transcription	Esophagus	oesophagus
19	chr8:90772000-90773000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr8:90772000-90773200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr8:90772000-90773200	Enhancers	HUVEC	blood vessel
22	chr8:90772000-90773400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:90772000-90773800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:90772000-90776200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr8:90772000-90777400	Weak transcription	Primary T cells from cord blood	blood
26	chr8:90772000-90778000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr8:90772000-90778400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr8:90772000-90784600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr8:90772000-90785000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr8:90772000-90785400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr8:90772000-90796800	Weak transcription	Lung	lung
32	chr8:90772000-90797000	Weak transcription	Ovary	ovary
33	chr8:90772200-90772800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr8:90772200-90772800	Weak transcription	HSMMtube	muscle
35	chr8:90772200-90773000	Enhancers	Brain Cingulate Gyrus	brain
36	chr8:90772200-90773200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr8:90772200-90773200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr8:90772200-90773200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr8:90772200-90773200	Enhancers	Brain Angular Gyrus	brain
40	chr8:90772200-90773600	Weak transcription	Stomach Mucosa	stomach
41	chr8:90772200-90773800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:90772200-90773800	Enhancers	Brain Substantia Nigra	brain
43	chr8:90772200-90774000	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr8:90772200-90774200	Enhancers	HepG2	liver
45	chr8:90772200-90774400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr8:90772200-90775800	Weak transcription	HSMM	muscle
47	chr8:90772200-90777600	Weak transcription	Placenta	Placenta
48	chr8:90772200-90778000	Weak transcription	Fetal Kidney	kidney
49	chr8:90772200-90778200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr8:90772200-90778200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links