Variant report

Variant	rs7754547
Chromosome Location	chr6:69347206-69347207
allele	G/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	RAD21	chr6:69342384-69347457	SK-N-SH	brain:	n/a	chr6:69345907-69345917 chr6:69345020-69345034 chr6:69344689-69344699 chr6:69343839-69343849 chr6:69345328-69345338
2	RFX5	chr6:69342558-69347581	SK-N-SH	brain:	n/a	chr6:69344290-69344305 chr6:69346927-69346936 chr6:69344290-69344305
3	TBL1XR1	chr6:69346982-69347314	K562	blood:	n/a	n/a
4	CEBPB	chr6:69347008-69347357	K562	blood:	n/a	chr6:69347170-69347183

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:69346849..69353858-chr6:69356877..69365508,11	K562	blood:

Variant related genes	Relation type
ENSG00000230910	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10945133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10945134	1.00[ASW][hapmap];0.82[EUR][1000 genomes]
rs12198214	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12211047	1.00[CHB][hapmap]
rs12216491	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17198341	1.00[CHB][hapmap]
rs2585619	0.81[EUR][1000 genomes]
rs2585620	0.82[EUR][1000 genomes]
rs2802690	0.81[EUR][1000 genomes]
rs2802704	0.83[EUR][1000 genomes]
rs2802705	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs4554295	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs7743914	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9346237	1.00[ASW][hapmap]

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	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv830680	chr6:69192214-69351103	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7754547	SMAP1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69342600-69349600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:69342600-69351000	Active TSS	Brain Angular Gyrus	brain
3	chr6:69342800-69348000	Active TSS	Fetal Brain Male	brain
4	chr6:69343000-69348000	Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr6:69343200-69348600	Active TSS	Brain Cingulate Gyrus	brain
6	chr6:69343200-69348800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:69343200-69349200	Active TSS	Brain Germinal Matrix	brain
8	chr6:69343200-69351200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:69343200-69352000	Active TSS	Brain Anterior Caudate	brain
10	chr6:69343400-69348400	Active TSS	Fetal Stomach	stomach
11	chr6:69343400-69349600	Active TSS	Fetal Brain Female	brain
12	chr6:69343600-69347400	Active TSS	Brain Substantia Nigra	brain
13	chr6:69343600-69348200	Active TSS	Right Atrium	heart
14	chr6:69343800-69347400	Active TSS	Colon Smooth Muscle	Colon
15	chr6:69346200-69347400	Active TSS	Stomach Smooth Muscle	stomach
16	chr6:69346200-69349000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:69346200-69349200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:69346200-69349200	Weak transcription	Pancreas	Pancrea
19	chr6:69346600-69347400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
20	chr6:69346600-69348000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:69346600-69349000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:69346600-69349000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:69346600-69349600	Weak transcription	Aorta	Aorta
24	chr6:69346800-69348000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
25	chr6:69346800-69350000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:69347000-69347400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:69347000-69347400	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr6:69347000-69347400	Bivalent/Poised TSS	Fetal Lung	lung
29	chr6:69347000-69348600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:69347000-69349800	Weak transcription	Right Ventricle	heart
31	chr6:69347200-69347400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
32	chr6:69347200-69349400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:69347200-69349400	Enhancers	K562	blood

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