Variant report

Variant	rs6852990
Chromosome Location	chr4:7803457-7803458
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	EP300	chr4:7803449-7803530	GM12878	blood:	n/a	n/a
2	RAD21	chr4:7803247-7804417	SK-N-SH	brain:	n/a	chr4:7804040-7804049 chr4:7804034-7804053

No.	Distal block	Cell Line	Cell type
1	chr4:7803065..7804892-chr4:7807691..7809470,2	K562	blood:
2	chr4:7803065..7805141-chr4:7807691..7809396,2	K562	blood:
3	chr4:7770365..7771286-chr4:7803447..7804040,2	MCF-7	breast:

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10029941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13109291	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1557817	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2018399	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2107182	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28475763	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs4388087	0.85[CHB][hapmap]
rs4404542	0.85[CHB][hapmap]
rs4413405	0.85[CHB][hapmap]
rs55689818	0.82[AFR][1000 genomes]
rs60840998	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6446619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs6827395	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6828807	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6829473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes]
rs6838291	0.82[CHB][hapmap]
rs756255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
2	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
5	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
7	chr4:7785800-7803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:7790800-7803600	Strong transcription	HSMM	muscle
11	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
12	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr4:7791400-7806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:7793200-7803800	Strong transcription	NH-A	brain
15	chr4:7794400-7803600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:7795600-7803800	Weak transcription	Fetal Kidney	kidney
17	chr4:7795800-7803800	Weak transcription	Fetal Heart	heart
18	chr4:7796800-7804200	Strong transcription	NHEK	skin
19	chr4:7797000-7807000	Weak transcription	Liver	Liver
20	chr4:7797200-7803800	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr4:7797800-7803600	Strong transcription	Fetal Muscle Leg	muscle
22	chr4:7798200-7807200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:7800000-7803600	Strong transcription	Hela-S3	cervix
24	chr4:7800200-7807200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:7800600-7805000	Weak transcription	Primary T cells from cord blood	blood
26	chr4:7800600-7806200	Weak transcription	Fetal Thymus	thymus
27	chr4:7800600-7828800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:7801000-7803800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:7801000-7804000	Strong transcription	Osteobl	bone
30	chr4:7801400-7807200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:7801400-7807400	Weak transcription	Right Ventricle	heart
32	chr4:7801800-7807400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:7802000-7806200	Weak transcription	Fetal Brain Male	brain
34	chr4:7802000-7807200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:7802000-7807200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:7802000-7807800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:7802200-7803800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr4:7802200-7805600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:7802200-7805600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:7802200-7806200	Weak transcription	Brain Substantia Nigra	brain
41	chr4:7802200-7819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:7802400-7803600	Enhancers	GM12878-XiMat	blood
43	chr4:7802400-7803800	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:7802400-7804800	Weak transcription	Colon Smooth Muscle	Colon
45	chr4:7802400-7805600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:7802400-7806000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:7802400-7806200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:7802400-7806600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr4:7802400-7806800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr4:7802400-7812400	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links