Variant report

Variant	rs2188964
Chromosome Location	chr7:125650488-125650489
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10230499	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10230735	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10251003	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10273785	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10276262	0.96[EUR][1000 genomes]
rs10277554	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10281122	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10487430	1.00[ASN][1000 genomes]
rs11770217	0.86[ASN][1000 genomes]
rs11771723	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11772077	0.86[ASN][1000 genomes]
rs11973855	0.86[ASN][1000 genomes]
rs12333418	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1362015	0.86[ASN][1000 genomes]
rs1362020	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1419531	0.87[EUR][1000 genomes]
rs16871585	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17149165	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17149168	1.00[ASN][1000 genomes]
rs17149198	1.00[ASN][1000 genomes]
rs17149212	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17149215	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2188965	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28526686	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28590172	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35073252	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35731602	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4489264	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4731283	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55659261	0.86[ASN][1000 genomes]
rs56076985	1.00[ASN][1000 genomes]
rs56210807	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56244439	1.00[ASN][1000 genomes]
rs57598547	1.00[ASN][1000 genomes]
rs58539609	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59933255	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60567342	1.00[ASN][1000 genomes]
rs61674002	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6467066	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6958279	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6965465	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6965646	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs719320	0.84[EUR][1000 genomes]
rs73720554	1.00[ASN][1000 genomes]
rs73720555	1.00[ASN][1000 genomes]
rs73720557	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73720566	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73720568	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73720569	1.00[ASN][1000 genomes]
rs73720579	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73720583	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs739687	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7779236	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7792657	0.91[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7797822	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7808742	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948720	chr7:124970772-125783434	Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1018428	chr7:125044642-125730775	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv889150	chr7:125232034-125716635	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv608349	chr7:125340641-125848851	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv889159	chr7:125418926-125927493	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv889161	chr7:125468407-125791900	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv429810	chr7:125488049-126131049	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv889162	chr7:125537419-125652488	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1022976	chr7:125542173-125976125	Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2761364	chr7:125545143-125664894	Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1032264	chr7:125545143-125665777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv525348	chr7:125566215-125733306	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv33257	chr7:125571419-125743350	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1032387	chr7:125575811-125743535	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv539115	chr7:125575811-125743535	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv608353	chr7:125576498-125724789	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv1025235	chr7:125579744-125688056	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv889163	chr7:125582500-125716635	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv889164	chr7:125582500-125791900	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	nsv1028186	chr7:125599204-125678628	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv518236	chr7:125601529-125730694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv1032930	chr7:125602535-125778020	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv608354	chr7:125607878-125761750	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	nsv889165	chr7:125607878-125791900	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	nsv1027916	chr7:125610829-125778020	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	nsv1018019	chr7:125619705-125743535	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv539116	chr7:125619705-125743535	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
28	nsv1019317	chr7:125619705-125810608	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
29	nsv539117	chr7:125619705-125810608	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
30	nsv608355	chr7:125623142-125777978	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
31	esv3584863	chr7:125625696-125735363	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
32	esv3584864	chr7:125625696-125751377	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
33	nsv518344	chr7:125644656-125730694	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2188964	TMEM229A	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:125642600-125653800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:125643000-125650600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:125643200-125657400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:125643400-125667000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:125646400-125687000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:125649200-125651600	Weak transcription	H9 Cell Line	embryonic stem cell

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