Variant report

Variant	rs10746436
Chromosome Location	chr1:212999701-212999702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212782226..212783823-chr1:212998854..213001770,2	K562	blood:
2	chr1:212984776..212986773-chr1:212997927..213000551,2	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10127459	1.00[ASN][1000 genomes]
rs10779594	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10864002	0.86[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs10864003	1.00[CEU][hapmap];1.00[CHB][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]
rs10864019	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11120033	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120034	0.80[AFR][1000 genomes]
rs11120038	0.81[AFR][1000 genomes]
rs11804466	1.00[CHB][hapmap]
rs11808834	1.00[CHB][hapmap]
rs11810592	1.00[CHB][hapmap]
rs12036735	1.00[ASN][1000 genomes]
rs12133194	0.83[AFR][1000 genomes]
rs12744555	0.86[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs12757944	0.83[AFR][1000 genomes]
rs1284800	1.00[ASN][1000 genomes]
rs1284864	1.00[ASN][1000 genomes]
rs15702	0.86[LWK][hapmap];0.91[YRI][hapmap]
rs1615680	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1692178	1.00[ASN][1000 genomes]
rs1692179	1.00[ASN][1000 genomes]
rs1692180	1.00[ASN][1000 genomes]
rs17019510	1.00[CHB][hapmap]
rs17020044	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17020046	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1770777	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1770778	1.00[ASN][1000 genomes]
rs1874419	1.00[ASN][1000 genomes]
rs2047289	1.00[ASN][1000 genomes]
rs2047293	1.00[ASN][1000 genomes]
rs2359321	1.00[CHB][hapmap]
rs2359324	1.00[ASN][1000 genomes]
rs2456815	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2644545	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2792558	1.00[ASN][1000 genomes]
rs2792560	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2792561	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2884675	0.83[AFR][1000 genomes]
rs35976699	1.00[ASN][1000 genomes]
rs3949369	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs41315581	1.00[ASN][1000 genomes]
rs4951639	0.88[LWK][hapmap];0.96[YRI][hapmap]
rs4951649	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs59252582	1.00[ASN][1000 genomes]
rs6540767	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6540768	1.00[ASN][1000 genomes]
rs6666362	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6667161	1.00[ASN][1000 genomes]
rs6674933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6681851	0.83[AFR][1000 genomes]
rs6685864	0.81[AFR][1000 genomes]
rs6686145	0.81[AFR][1000 genomes]
rs6689134	1.00[ASN][1000 genomes]
rs6689799	0.83[AFR][1000 genomes]
rs6696870	0.88[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6703612	1.00[ASN][1000 genomes]
rs7518378	1.00[CHB][hapmap]
rs7528119	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7528303	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs7533932	1.00[ASN][1000 genomes]
rs7542906	1.00[ASN][1000 genomes]
rs963327	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	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv549149	chr1:212997385-213009657	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
5	nsv508691	chr1:212998319-213028392	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
6	nsv549150	chr1:212999701-213011812	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10746436	NSL1	cis	lymphoblastoid	seeQTL
rs10746436	C1orf227	cis	lymphoblastoid	seeQTL
rs10746436	INTS7	cis	cerebellum	SCAN
rs10746436	NSL1	cis	parietal	SCAN
rs10746436	LOC642946	cis	multi-tissue	Pritchard
rs10746436	PTPN14	cis	cerebellum	SCAN
rs10746436	C1orf48	cis	multi-tissue	Pritchard
rs10746436	NSL1	cis	brain	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:212980800-213001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:212997200-213000200	ZNF genes & repeats	Fetal Intestine Small	intestine
4	chr1:212998600-212999800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:212998600-212999800	ZNF genes & repeats	HepG2	liver
6	chr1:212998600-212999800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr1:212998800-212999800	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr1:212998800-212999800	ZNF genes & repeats	Stomach Mucosa	stomach
9	chr1:212999000-212999800	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:212999400-213009400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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