Variant report

Variant	rs41385746
Chromosome Location	chr2:54305030-54305031
allele	C/T
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	CCNT2	chr2:54304409-54305033	K562	blood:	n/a	n/a
2	CBX3	chr2:54304442-54305141	K562	blood:	n/a	n/a
3	STAT5A	chr2:54304350-54305038	K562	blood:	n/a	n/a
4	TEAD4	chr2:54304176-54305098	K562	blood:	n/a	n/a
5	GATA1	chr2:54303036-54305151	K562	blood:	n/a	chr2:54303340-54303356 chr2:54303343-54303352
6	CBX3	chr2:54304383-54305691	K562	blood:	n/a	n/a
7	TRIM28	chr2:54304292-54305095	K562	blood:	n/a	n/a
8	KAP1	chr2:54303931-54305108	K562	blood:	n/a	n/a
9	GATA1	chr2:54303035-54305088	PBDE	blood:	n/a	chr2:54303340-54303356 chr2:54303343-54303352
10	ZNF384	chr2:54304482-54305094	K562	blood:	n/a	n/a
11	RFX5	chr2:54304592-54305051	K562	blood:	n/a	n/a
12	NR2F2	chr2:54304262-54305082	K562	blood:	n/a	n/a
13	SETDB1	chr2:54304577-54305075	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54303310..54306490-chr2:54307537..54312281,6	K562	blood:
2	chr2:54303600..54306437-chr2:54307043..54310223,4	K562	blood:
3	chr2:54304842..54306570-chr2:54310702..54313482,3	K562	blood:
4	chr2:54299748..54301680-chr2:54304103..54306352,2	K562	blood:

Variant related genes	Relation type
ENSG00000272156	TF binding region
ENSG00000272156	Chromatin interaction
ENSG00000241114	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1058320	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs1075265	0.94[CHB][hapmap]
rs10865277	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865278	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865279	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11125520	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695734	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11887549	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11896781	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1215150	0.81[CHB][hapmap]
rs1363062	0.88[CHB][hapmap];0.92[CHD][hapmap]
rs1363063	0.86[JPT][hapmap]
rs1421617	0.86[JPT][hapmap]
rs1559037	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1727522	0.81[CHB][hapmap]
rs1833497	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1833498	0.81[ASN][1000 genomes]
rs1862121	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1862122	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2018747	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2287642	0.88[CHB][hapmap]
rs2357954	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34769118	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671178	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671190	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4671872	0.94[CHB][hapmap]
rs56001939	0.85[AMR][1000 genomes]
rs62137965	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62137973	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6545384	0.81[ASN][1000 genomes]
rs6545388	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs6741891	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs718872	0.82[CHB][hapmap]
rs7558126	0.88[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7560947	0.80[ASN][1000 genomes]
rs7566894	0.88[CHB][hapmap]
rs7574477	0.82[CHB][hapmap]
rs7590846	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7591194	0.80[ASN][1000 genomes]
rs7600141	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7604357	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs805322	0.82[CHB][hapmap]
rs805367	0.82[CHB][hapmap]
rs805410	0.82[CHB][hapmap]
rs805412	0.82[CHB][hapmap]
rs805423	0.82[CHB][hapmap]
rs843677	0.81[CHB][hapmap]
rs888635	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs918357	0.88[CHB][hapmap];0.89[CHD][hapmap];0.80[MEX][hapmap]
rs929734	0.88[CHB][hapmap]
rs959285	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs959286	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41385746	PSME4	cis	cerebellum	SCAN
rs41385746	MTIF2	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54280800-54310000	Weak transcription	Ovary	ovary
2	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
3	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
5	chr2:54281600-54308800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:54287000-54310000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:54287200-54307000	Weak transcription	Primary T cells from cord blood	blood
8	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
9	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:54292000-54308400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:54293000-54306000	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:54293200-54306200	Weak transcription	Brain Anterior Caudate	brain
13	chr2:54293200-54306200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:54293400-54308400	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:54293600-54310600	Weak transcription	HSMM	muscle
16	chr2:54294800-54315000	Weak transcription	Fetal Intestine Small	intestine
17	chr2:54295200-54312200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:54295400-54309800	Weak transcription	Fetal Brain Male	brain
19	chr2:54301600-54308200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:54302200-54308200	Weak transcription	HMEC	breast
21	chr2:54302200-54310600	Weak transcription	A549	lung
22	chr2:54302600-54308600	Weak transcription	NH-A	brain
23	chr2:54302600-54310400	Weak transcription	Osteobl	bone
24	chr2:54302800-54317800	Weak transcription	Left Ventricle	heart
25	chr2:54303400-54305400	Flanking Active TSS	K562	blood
26	chr2:54305000-54306200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:54305000-54308000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:54305000-54315000	Weak transcription	Fetal Intestine Large	intestine
29	chr2:54305000-54315200	Weak transcription	Pancreas	Pancrea

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