Variant report

Variant	rs10496323
Chromosome Location	chr2:98289839-98289840
allele	C/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	MAZ	chr2:98289648-98290809	K562	blood:	n/a	chr2:98290432-98290441
2	ATF1	chr2:98289774-98290894	K562	blood:	n/a	n/a
3	POLR2A	chr2:98289603-98290667	K562	blood:	n/a	n/a
4	MAX	chr2:98289605-98290405	K562	blood:	n/a	n/a
5	UBTF	chr2:98289659-98290738	K562	blood:	n/a	n/a
6	POLR2A	chr2:98289675-98290632	K562	blood:	n/a	n/a
7	CBX3	chr2:98289713-98290370	K562	blood:	n/a	n/a
8	JUND	chr2:98289605-98290765	K562	blood:	n/a	chr2:98289770-98289781 chr2:98289771-98289780 chr2:98289773-98289780
9	CUX1	chr2:98289765-98290963	K562	blood:	n/a	n/a
10	RCOR1	chr2:98289690-98290801	K562	blood:	n/a	n/a
11	BHLHE40	chr2:98289690-98290897	K562	blood:	n/a	n/a
12	MAX	chr2:98289707-98290601	K562	blood:	n/a	chr2:98290432-98290441
13	RCOR1	chr2:98289705-98290495	K562	blood:	n/a	n/a
14	ELF1	chr2:98289603-98289887	K562	blood:	n/a	chr2:98289697-98289710
15	TBL1XR1	chr2:98289664-98290516	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:98286306..98287909-chr2:98288768..98291732,2	MCF-7	breast:
2	chr2:98277787..98279697-chr2:98287927..98289913,2	MCF-7	breast:
3	chr2:98277540..98280673-chr2:98288354..98290107,4	K562	blood:
4	chr2:98261015..98264268-chr2:98289158..98291782,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZAP70-2	chr2:98289635-98292184	NONHSAT072675
2	lnc-ZAP70-2	chr2:98289635-98291020	NONHSAT072676

Variant related genes	Relation type
LINC01125	TF binding region
ENSG00000115073	Chromatin interaction
ENSG00000228486	Chromatin interaction
ENSG00000135940	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1020396	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[LWK][hapmap];0.89[ASN][1000 genomes]
rs1042705	0.81[CHB][hapmap]
rs11123849	0.81[CHB][hapmap]
rs11123861	1.00[ASW][hapmap];0.84[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11547232	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680855	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11690658	0.92[CEU][hapmap]
rs11691779	0.82[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs11893601	0.81[CHB][hapmap]
rs11894651	0.81[CHB][hapmap]
rs12994535	0.92[CEU][hapmap]
rs12994966	0.92[ASN][1000 genomes]
rs12997695	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13000505	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13001728	0.95[CEU][hapmap]
rs13003963	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13027550	0.82[AMR][1000 genomes]
rs13034349	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.92[ASN][1000 genomes]
rs1463173	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1463174	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1800649	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823324	0.81[CHB][hapmap]
rs1965204	0.91[CEU][hapmap]
rs2053824	0.81[CHB][hapmap]
rs2276645	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2290124	0.81[CHB][hapmap]
rs35211079	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3931133	0.91[CEU][hapmap]
rs4086889	0.81[AMR][1000 genomes]
rs55772322	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56281704	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62157580	0.97[ASN][1000 genomes]
rs6718109	0.92[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv3451326	chr2:98289174-98304076	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10496323	CNNM3	cis	cerebellum	SCAN
rs10496323	ANKRD36B	cis	Thyroid	GTEx
rs10496323	ANKRD39	cis	cerebellum	SCAN
rs10496323	ANKRD36B	cis	Skin Sun Exposed Lower leg	GTEx
rs10496323	ANKRD36B	cis	lung	GTEx
rs10496323	ANKRD36B	cis	Stomach	GTEx
rs10496323	ANKRD36B	cis	cerebellum	SCAN
rs10496323	ANKRD36B	cis	Nerve Tibial	GTEx
rs10496323	ANKRD36B	cis	Esophagus Mucosa	GTEx
rs10496323	ANKRD36B	cis	Adipose Subcutaneous	GTEx
rs10496323	ANKRD36B	cis	Artery Tibial	GTEx
rs10496323	AC017099.3	cis	Muscle Skeletal	GTEx
rs10496323	ZAP70	cis	cerebellum	SCAN
rs10496323	ACTR1B	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98281000-98290400	Weak transcription	Spleen	Spleen
2	chr2:98281000-98323800	Weak transcription	Gastric	stomach
3	chr2:98281400-98290000	Weak transcription	Left Ventricle	heart
4	chr2:98281400-98295200	Weak transcription	Esophagus	oesophagus
5	chr2:98281600-98290000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:98281600-98290200	Weak transcription	Pancreas	Pancrea
7	chr2:98281600-98290400	Weak transcription	Thymus	Thymus
8	chr2:98281600-98291400	Weak transcription	Right Atrium	heart
9	chr2:98281600-98292000	Weak transcription	Adipose Nuclei	Adipose
10	chr2:98281600-98292800	Weak transcription	HSMM	muscle
11	chr2:98281600-98293200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:98281600-98294800	Weak transcription	Brain Anterior Caudate	brain
13	chr2:98281600-98295400	Weak transcription	Right Ventricle	heart
14	chr2:98281600-98298800	Weak transcription	Aorta	Aorta
15	chr2:98281800-98293800	Weak transcription	Brain Angular Gyrus	brain
16	chr2:98281800-98296200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:98281800-98296200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:98282000-98290000	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:98282000-98292000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:98282000-98293800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:98285600-98292200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:98286200-98292000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:98288600-98293600	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:98289200-98290000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:98289200-98291600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:98289200-98292000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:98289400-98290400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:98289400-98292200	Enhancers	Primary hematopoietic stem cells	blood
29	chr2:98289600-98290000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:98289600-98290400	Enhancers	Fetal Thymus	thymus
31	chr2:98289600-98290400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr2:98289600-98291600	Enhancers	GM12878-XiMat	blood
33	chr2:98289800-98290600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr2:98289800-98291000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:98289800-98291000	Flanking Active TSS	K562	blood
36	chr2:98289800-98293600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links