Variant report

Variant	rs9879452
Chromosome Location	chr3:194870655-194870656
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	POLR2A	chr3:194870649-194871834	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:194870527-194871913	GM12892	blood:	n/a	n/a
3	TEAD4	chr3:194870629-194871694	K562	blood:	n/a	n/a
4	CEBPB	chr3:194870532-194871828	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:194868265-194872140	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:194868269-194872203	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:194868355-194872209	HUVEC	blood vessel:	n/a	n/a
8	CHD1	chr3:194868421-194871809	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:194870573-194870940	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:194870510-194871879	GM12892	blood:	n/a	n/a
11	NFATC1	chr3:194870293-194872040	GM12878	blood:	n/a	n/a
12	MAFK	chr3:194870622-194871623	K562	blood:	n/a	n/a
13	RCOR1	chr3:194870648-194871869	IMR90	lung:	n/a	n/a
14	POLR2A	chr3:194870114-194872071	GM19193	blood:	n/a	n/a
15	WRNIP1	chr3:194870098-194872012	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:194868262-194872259	HUVEC	blood vessel:	n/a	n/a
17	CBX3	chr3:194870636-194871809	K562	blood:	n/a	n/a
18	POLR2A	chr3:194869898-194871874	HUVEC	blood vessel:	n/a	n/a
19	RUNX3	chr3:194870643-194871909	GM12878	blood:	n/a	n/a
20	MTA3	chr3:194870649-194871976	GM12878	blood:	n/a	n/a
21	MAZ	chr3:194870075-194870661	GM12878	blood:	n/a	n/a
22	MXI1	chr3:194870650-194870703	K562	blood:	n/a	n/a
23	ZNF143	chr3:194870557-194871899	GM12878	blood:	n/a	chr3:194871685-194871703
24	STAT5A	chr3:194870644-194871829	GM12878	blood:	n/a	chr3:194871796-194871808
25	POLR2A	chr3:194869919-194871774	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:194869872-194872144	GM12878	blood:	n/a	n/a
27	MAZ	chr3:194870628-194872279	IMR90	lung:	n/a	chr3:194871800-194871810
28	POLR2A	chr3:194870629-194871137	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:194868342-194871929	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:194868149-194872233	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr3:194870107-194871896	GM12878	blood:	n/a	n/a
32	ZMIZ1	chr3:194870608-194871705	K562	blood:	n/a	n/a
33	MTA3	chr3:194868157-194872051	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:194870589-194871876	GM12892	blood:	n/a	n/a
35	EBF1	chr3:194870569-194871957	GM12878	blood:	n/a	chr3:194871110-194871123 chr3:194871111-194871121 chr3:194871110-194871121 chr3:194871112-194871121
36	MYC	chr3:194870540-194870676	K562	blood:	n/a	n/a
37	GATA2	chr3:194869980-194871824	HUVEC	blood vessel:	n/a	chr3:194870039-194870055 chr3:194871667-194871675 chr3:194871304-194871321 chr3:194871298-194871312 chr3:194870529-194870546 chr3:194870336-194870346 chr3:194870540-194870547 chr3:194870533-194870554 chr3:194870540-194870547 chr3:194871303-194871312 chr3:194870540-194870547
38	GATA2	chr3:194869873-194870780	SH-SY5Y	brain:	n/a	chr3:194870039-194870055 chr3:194870529-194870546 chr3:194870336-194870346 chr3:194870540-194870547 chr3:194870533-194870554 chr3:194870540-194870547 chr3:194870540-194870547
39	FOXM1	chr3:194870544-194871381	GM12878	blood:	n/a	n/a
40	GATA1	chr3:194870021-194871971	PBDE	blood:	n/a	chr3:194870039-194870055 chr3:194871667-194871675 chr3:194871304-194871321 chr3:194870529-194870546 chr3:194870336-194870346 chr3:194870540-194870547 chr3:194870533-194870554 chr3:194870540-194870547 chr3:194871303-194871312 chr3:194870540-194870547
41	GATA3	chr3:194869425-194870681	SH-SY5Y	brain:	n/a	chr3:194870039-194870055 chr3:194870529-194870546 chr3:194870336-194870346 chr3:194870540-194870547 chr3:194870533-194870554 chr3:194870540-194870547 chr3:194870540-194870547

No.	Distal block	Cell Line	Cell type
1	chr3:194869726..194872527-chr3:194883949..194885510,2	K562	blood:
2	chr3:194870262..194872274-chr3:194880520..194882642,2	K562	blood:
3	chr3:194870603..194872968-chr3:194930308..194933039,3	K562	blood:
4	chr3:194868967..194870771-chr3:194979716..194982181,2	K562	blood:
5	chr3:194870056..194873329-chr3:194873550..194878227,7	K562	blood:

Variant related genes	Relation type
RN7SL36P	TF binding region
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4677812	0.89[YRI][hapmap]
rs7646496	0.82[AFR][1000 genomes]
rs903310	0.89[MKK][hapmap];0.80[YRI][hapmap]
rs9288754	0.84[TSI][hapmap]
rs9825174	0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer 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
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9879452	RPL35A	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194841000-194872800	Weak transcription	HSMMtube	muscle
2	chr3:194854600-194871000	Weak transcription	Fetal Brain Female	brain
3	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
4	chr3:194861200-194872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:194861600-194870800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:194861800-194870800	Weak transcription	Aorta	Aorta
7	chr3:194861800-194871000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:194861800-194871200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:194861800-194872800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:194861800-194875000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:194862400-194897800	Weak transcription	Dnd41	blood
12	chr3:194864400-194870800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:194865000-194871000	Enhancers	Fetal Thymus	thymus
14	chr3:194867200-194871800	Enhancers	Spleen	Spleen
15	chr3:194867400-194871000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:194867600-194871000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:194867800-194872000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:194867800-194872400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:194868000-194870800	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:194868200-194871000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:194868200-194871400	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr3:194868200-194871800	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr3:194868200-194872000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr3:194868200-194872200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr3:194868200-194872200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:194868200-194877800	Enhancers	Fetal Stomach	stomach
27	chr3:194868400-194870800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:194868400-194870800	Enhancers	Fetal Lung	lung
29	chr3:194868400-194871000	Enhancers	H1 Cell Line	embryonic stem cell
30	chr3:194868400-194871000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr3:194868400-194871000	Flanking Active TSS	HUVEC	blood vessel
32	chr3:194868400-194872000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:194868400-194877400	Enhancers	Fetal Heart	heart
34	chr3:194868600-194870800	Weak transcription	Brain Anterior Caudate	brain
35	chr3:194868600-194871000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:194868600-194871000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:194868600-194871800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:194868800-194871000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr3:194868800-194871000	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr3:194868800-194871000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:194868800-194871000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:194868800-194871000	Enhancers	Adipose Nuclei	Adipose
43	chr3:194868800-194871000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:194868800-194871000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr3:194868800-194871200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:194868800-194875000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:194868800-194885400	Enhancers	Fetal Muscle Leg	muscle
48	chr3:194869000-194870800	Weak transcription	Gastric	stomach
49	chr3:194869000-194870800	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr3:194869000-194871000	Enhancers	Primary B cells from peripheral blood	blood

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