Variant report

Variant	rs12746613
Chromosome Location	chr1:161467042-161467043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161461950..161465186-chr1:161466189..161468488,5	K562	blood:
2	chr1:161466769..161469668-chr1:161480894..161483734,2	K562	blood:
3	chr1:161463735..161467161-chr1:161469727..161472707,3	K562	blood:
4	chr1:161466032..161468189-chr1:161717576..161719552,2	K562	blood:
5	chr1:161441922..161445226-chr1:161466780..161470505,3	K562	blood:
6	chr1:161466774..161469525-chr1:161472728..161476686,5	K562	blood:

Variant related genes	Relation type
ENSG00000143226	Chromatin interaction
ENSG00000273112	Chromatin interaction
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10494359	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494360	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801022	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs11810143	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12722986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731669	0.83[CEU][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes]
rs12741391	1.00[ASN][1000 genomes]
rs12744234	1.00[ASN][1000 genomes]
rs12748656	1.00[ASN][1000 genomes]
rs12749237	1.00[ASN][1000 genomes]
rs12758795	1.00[ASN][1000 genomes]
rs17394957	1.00[ASN][1000 genomes]
rs17395595	1.00[ASN][1000 genomes]
rs17398689	1.00[ASN][1000 genomes]
rs17399583	1.00[ASN][1000 genomes]
rs17400053	1.00[ASN][1000 genomes]
rs17400517	1.00[ASN][1000 genomes]
rs34006306	1.00[ASN][1000 genomes]
rs34370781	1.00[ASN][1000 genomes]
rs34550741	1.00[ASN][1000 genomes]
rs35046931	1.00[ASN][1000 genomes]
rs35200803	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35620439	1.00[ASN][1000 genomes]
rs35825219	1.00[ASN][1000 genomes]
rs35949692	1.00[ASN][1000 genomes]
rs36059328	1.00[ASN][1000 genomes]
rs373579	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs3845548	1.00[ASN][1000 genomes]
rs4082014	1.00[ASN][1000 genomes]
rs4657086	1.00[ASN][1000 genomes]
rs55864322	1.00[ASN][1000 genomes]
rs55971447	1.00[ASN][1000 genomes]
rs56157533	1.00[ASN][1000 genomes]
rs56199187	1.00[ASN][1000 genomes]
rs61686728	1.00[ASN][1000 genomes]
rs61802846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66579967	1.00[ASN][1000 genomes]
rs6664924	0.89[EUR][1000 genomes]
rs6666989	1.00[ASN][1000 genomes]
rs6671753	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679543	1.00[ASN][1000 genomes]
rs66888136	1.00[ASN][1000 genomes]
rs67307769	1.00[ASN][1000 genomes]
rs67418890	1.00[ASN][1000 genomes]
rs71632979	1.00[ASN][1000 genomes]
rs71632995	1.00[ASN][1000 genomes]
rs71639056	1.00[ASN][1000 genomes]
rs71639062	1.00[ASN][1000 genomes]
rs72714962	1.00[ASN][1000 genomes]
rs72717013	1.00[ASN][1000 genomes]
rs72717016	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72717018	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72717040	1.00[ASN][1000 genomes]
rs72717048	1.00[ASN][1000 genomes]
rs7515174	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518087	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529225	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529425	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532275	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539468	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552317	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867624	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427039	1.00[ASN][1000 genomes]
rs9427059	1.00[ASN][1000 genomes]
rs9427065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427372	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9427387	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9427392	1.00[ASN][1000 genomes]
rs9427394	1.00[ASN][1000 genomes]
rs9427398	1.00[ASN][1000 genomes]
rs9427399	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427400	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427401	0.83[CEU][hapmap];1.00[ASN][1000 genomes]
rs9427402	1.00[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	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv432998	chr1:161335902-161673682	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv433009	chr1:161343927-161639328	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1005812	chr1:161343951-161548101	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv535182	chr1:161343951-161548101	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	esv2756866	chr1:161344255-161681552	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
7	esv2758972	chr1:161344255-161681552	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv433020	chr1:161355634-161673682	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
9	esv2754329	chr1:161355728-161673682	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
10	nsv433031	chr1:161355728-161673682	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
11	nsv433042	chr1:161372038-161673682	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv433053	chr1:161389417-161673682	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv3243	chr1:161391435-161476893	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv433075	chr1:161395555-161673682	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv831725	chr1:161403030-161666732	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
16	esv2757757	chr1:161406313-161624427	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
18	esv1821964	chr1:161410458-161642332	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
19	esv18665	chr1:161411989-161544650	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	esv1812323	chr1:161413114-161624425	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	esv1814016	chr1:161413114-161624425	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	nsv427841	chr1:161413114-161624425	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv831736	chr1:161413123-161624424	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	esv1824713	chr1:161414555-161642332	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
25	esv1821631	chr1:161414640-161644896	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
26	esv2750812	chr1:161463498-161639559	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
27	esv2752696	chr1:161463498-161639559	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
28	esv2750813	chr1:161463498-161673682	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
29	esv2750814	chr1:161463498-161673682	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
30	esv2755678	chr1:161463498-161678377	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
31	esv2752664	chr1:161463601-161673682	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
32	esv2756399	chr1:161463814-161639559	Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
33	nsv433086	chr1:161465420-161639559	Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12746613	MEF2D	cis	cerebellum	SCAN
rs12746613	FCGR2A	cis	lymphoblastoid	seeQTL
rs12746613	PVRL4	cis	cerebellum	SCAN
rs12746613	OR10J1	cis	cerebellum	SCAN
rs12746613	FCGR2B	cis	multi-tissue	Pritchard
rs12746613	HSPA6	cis	multi-tissue	Pritchard
rs12746613	FCGR2A	cis	multi-tissue	Pritchard
rs12746613	RXFP4	cis	parietal	SCAN
rs12746613	FCGR2B	cis	Whole Blood	GTEx
rs12746613	C1orf61	cis	cerebellum	SCAN
rs12746613	FCGR2C	cis	Muscle Skeletal	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161462400-161467800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:161464400-161467200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:161464600-161468400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:161465800-161468600	Weak transcription	K562	blood
5	chr1:161466000-161467600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:161466600-161471400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:161467000-161467800	Enhancers	Skeletal Muscle Male	skeletal muscle

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