Variant report

Variant	rs3746250
Chromosome Location	chr19:35835582-35835583
allele	A/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	POLR2A	chr19:35834081-35844229	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:35834201-35836155	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:35834959-35836079	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:35835109-35836104	GM18505	blood:	n/a	n/a
5	POLR2A	chr19:35834730-35836134	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:35834068-35836071	GM12891	blood:	n/a	n/a
7	POLR2A	chr19:35835045-35835995	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:35835186-35836011	GM15510	blood:	n/a	n/a
9	POLR2A	chr19:35835109-35836122	GM12878	blood:	n/a	n/a
10	MTA3	chr19:35835017-35835848	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:35834892-35836156	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:35835495-35835932	GM12878	blood:	n/a	n/a
13	PML	chr19:35834990-35836085	GM12878	blood:	n/a	n/a
14	NFATC1	chr19:35835252-35835645	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:35835054-35835947	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:35834959-35844013	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:35835089-35836053	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:35835179-35835994	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:35834030-35836136	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:35835168-35835978	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:35835109-35836101	GM19193	blood:	n/a	n/a

Variant related genes	Relation type
CD22	TF binding region
MIR5196	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2901967	1.00[YRI][hapmap]
rs3458	1.00[YRI][hapmap]
rs6510478	0.81[EUR][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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
8	esv1828194	chr19:35812566-35865695	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067129	chr19:35827036-35849310	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3746250	KCNN4	cis	cerebellum	SCAN
rs3746250	LGALS17A	cis	parietal	SCAN
rs3746250	TBCB	cis	cerebellum	SCAN
rs3746250	CD22	cis	Thyroid	GTEx
rs3746250	RPS16	cis	parietal	SCAN
rs3746250	CYP2A7	cis	parietal	SCAN
rs3746250	PRX	cis	cerebellum	SCAN
rs3746250	MAG	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35817600-35844000	Weak transcription	Brain Angular Gyrus	brain
2	chr19:35818800-35836600	Weak transcription	Brain Anterior Caudate	brain
3	chr19:35824200-35837000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:35825400-35838200	Genic enhancers	Primary B cells from peripheral blood	blood
5	chr19:35825400-35838200	Strong transcription	Ovary	ovary
6	chr19:35828400-35838200	Strong transcription	Brain Hippocampus Middle	brain
7	chr19:35828600-35836400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:35829600-35836800	Weak transcription	HepG2	liver
9	chr19:35830200-35836800	Strong transcription	Brain Substantia Nigra	brain
10	chr19:35832000-35836800	Strong transcription	Brain Cingulate Gyrus	brain
11	chr19:35832600-35836600	Weak transcription	K562	blood
12	chr19:35832800-35838800	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr19:35833000-35836400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr19:35833000-35836600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr19:35833200-35837000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:35834200-35837200	Genic enhancers	Primary B cells from cord blood	blood
17	chr19:35835200-35835600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:35835200-35836400	Genic enhancers	GM12878-XiMat	blood
19	chr19:35835400-35835800	Genic enhancers	Spleen	Spleen
20	chr19:35835400-35838000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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