Variant report

Variant	rs4900692
Chromosome Location	chr14:37663548-37663549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:37662314..37664941-chr14:37664960..37666969,2	K562	blood:
2	chr14:37639617..37644848-chr14:37662875..37669924,15	K562	blood:
3	chr14:37639061..37645694-chr14:37661777..37669317,18	MCF-7	breast:
4	chr14:37641298..37642813-chr14:37662827..37664578,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258708	Chromatin interaction
ENSG00000183032	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10132070	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10135285	1.00[ASW][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10136217	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10136464	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10137231	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10139240	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10139649	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10140175	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10141058	0.80[MEX][hapmap]
rs10145536	0.82[MKK][hapmap]
rs10148078	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10150704	0.93[ASW][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1080374	0.96[ASN][1000 genomes]
rs1117024	0.96[ASN][1000 genomes]
rs11850049	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11850688	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12882311	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12883655	0.96[ASN][1000 genomes]
rs12883794	0.96[ASN][1000 genomes]
rs12884046	0.96[ASN][1000 genomes]
rs12891038	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12897482	0.81[EUR][1000 genomes]
rs1403	0.80[EUR][1000 genomes]
rs1535137	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17554224	0.85[CEU][hapmap]
rs2093119	0.93[ASW][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2415389	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28663019	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34123291	0.94[ASN][1000 genomes]
rs34138206	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34164918	0.83[EUR][1000 genomes]
rs34360521	0.94[ASN][1000 genomes]
rs34503846	0.81[EUR][1000 genomes]
rs34613310	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35127962	0.82[EUR][1000 genomes]
rs35322850	0.95[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35412613	0.80[EUR][1000 genomes]
rs35799924	0.80[EUR][1000 genomes]
rs3861484	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4344641	0.87[EUR][1000 genomes]
rs4522325	0.82[EUR][1000 genomes]
rs4605060	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61988264	0.96[ASN][1000 genomes]
rs61988280	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61988282	0.81[EUR][1000 genomes]
rs61988284	0.83[EUR][1000 genomes]
rs61988286	0.83[EUR][1000 genomes]
rs61988287	0.83[EUR][1000 genomes]
rs61988304	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61988307	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6571791	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6571792	0.96[ASN][1000 genomes]
rs6571793	0.96[ASN][1000 genomes]
rs6571794	0.96[ASN][1000 genomes]
rs6571798	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68051257	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714229	0.93[ASW][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs714230	0.87[ASW][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7142673	0.93[ASW][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7142924	0.96[ASN][1000 genomes]
rs7143494	0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7143703	0.96[ASN][1000 genomes]
rs7143872	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7143938	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs7145475	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7145768	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7146935	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7148710	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7149939	0.93[ASW][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7151191	0.85[GIH][hapmap]
rs7151497	0.93[ASW][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7151519	0.94[ASN][1000 genomes]
rs7153180	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap]
rs7157361	0.96[ASN][1000 genomes]
rs7161425	0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72671718	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8004700	0.96[ASN][1000 genomes]
rs8005945	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8006144	0.81[EUR][1000 genomes]
rs8007251	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8011459	0.91[ASN][1000 genomes]
rs8012018	0.92[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8012643	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8014303	0.96[ASN][1000 genomes]
rs8015022	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8015159	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8015843	0.96[ASN][1000 genomes]
rs8016262	0.96[ASN][1000 genomes]
rs8018823	0.95[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8019549	0.93[ASW][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8019652	0.80[EUR][1000 genomes]
rs8019950	0.90[ASN][1000 genomes]
rs8021181	0.83[EUR][1000 genomes]
rs8022156	0.83[EUR][1000 genomes]
rs910509	0.93[ASW][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9322977	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534288	chr14:37254539-37697745	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1050174	chr14:37556357-37664143	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1043410	chr14:37556357-37671059	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv915783	chr14:37607836-38002966	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1036854	chr14:37609535-38013533	Active TSS ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv542045	chr14:37609535-38013533	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv901635	chr14:37623177-37782273	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3528451	chr14:37631483-37771365	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	esv3527359	chr14:37631504-37771435	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	esv3370191	chr14:37631508-37771354	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	esv3527360	chr14:37631521-37771311	Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv3528462	chr14:37631535-37771345	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	esv3528473	chr14:37631543-37771255	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	esv3527361	chr14:37631554-37771408	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	esv3528484	chr14:37631599-37771228	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv3527363	chr14:37631608-37771230	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	esv3367731	chr14:37642250-37668518	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4900692	TRAPPC6B	cis	cerebellum	SCAN
rs4900692	NKX2-8	cis	parietal	SCAN
rs4900692	SLC2A2	trans	cerebellum	SCAN
rs4900692	SEC23A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:37657400-37666600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:37657800-37666600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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