Variant report

Variant	rs12121310
Chromosome Location	chr1:161719215-161719216
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:80)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:80 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161719212-161720281	GM12891	blood:	n/a	n/a
2	GATA1	chr1:161719144-161720423	PBDE	blood:	n/a	n/a
3	NFIC	chr1:161719184-161720305	GM12878	blood:	n/a	n/a
4	CEBPB	chr1:161719088-161720034	GM12878	blood:	n/a	n/a
5	PML	chr1:161719064-161720325	GM12878	blood:	n/a	n/a
6	SP2	chr1:161719143-161719855	HepG2	liver:	n/a	chr1:161719423-161719446
7	POLR2A	chr1:161719116-161720332	MCF10A-Er-Src	breast:	n/a	n/a
8	YY1	chr1:161719196-161720322	H1-hESC	embryonic stem cell:	n/a	n/a
9	STAT5A	chr1:161719179-161720343	K562	blood:	n/a	n/a
10	POLR2A	chr1:161719135-161720433	MCF10A-Er-Src	breast:	n/a	n/a
11	MXI1	chr1:161719111-161720413	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:161719196-161720265	SK-N-SH	brain:	n/a	n/a
13	MAX	chr1:161719169-161720428	A549	lung:	n/a	chr1:161720169-161720179 chr1:161720054-161720064
14	POLR2A	chr1:161719176-161720305	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr1:161719080-161719230	HPAF	blood vessel:	n/a	n/a
16	JUN	chr1:161719204-161719673	H1-hESC	embryonic stem cell:	n/a	n/a
17	ELF1	chr1:161719143-161720269	MCF-7	breast:	n/a	chr1:161720166-161720178
18	YY1	chr1:161719176-161720327	SK-N-SH_RA	brain:	n/a	chr1:161719190-161719198
19	YY1	chr1:161719199-161720262	GM12878	blood:	n/a	n/a
20	BCL3	chr1:161719140-161720104	A549	lung:	n/a	chr1:161720049-161720062 chr1:161719434-161719443
21	MAFK	chr1:161719161-161719786	K562	blood:	n/a	n/a
22	TEAD4	chr1:161719131-161720471	K562	blood:	n/a	n/a
23	EBF1	chr1:161719202-161720345	GM12878	blood:	n/a	chr1:161719517-161719526 chr1:161719517-161719527 chr1:161719516-161719527 chr1:161719515-161719528
24	YY1	chr1:161719191-161720278	K562	blood:	n/a	n/a
25	POLR2A	chr1:161719213-161720478	K562	blood:	n/a	n/a
26	HCFC1	chr1:161718893-161720620	Hela-S3	cervix:	n/a	n/a
27	MAX	chr1:161719205-161720229	MCF-7	breast:	n/a	chr1:161720169-161720179 chr1:161720054-161720064
28	TEAD4	chr1:161719209-161719719	HepG2	liver:	n/a	n/a
29	NR2F2	chr1:161719156-161720424	K562	blood:	n/a	n/a
30	POLR2A	chr1:161718920-161720671	PFSK-1	brain:	n/a	n/a
31	GABPA	chr1:161719204-161720191	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr1:161719159-161720248	Hela-S3	cervix:	n/a	n/a
33	TCF12	chr1:161719155-161720434	A549	lung:	n/a	n/a
34	EP300	chr1:161719174-161720105	ECC-1	luminal epithelium:	n/a	n/a
35	ZNF143	chr1:161719190-161720334	K562	blood:	n/a	n/a
36	POLR2A	chr1:161719032-161720401	U87	brain:	n/a	n/a
37	POLR2A	chr1:161719214-161720186	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr1:161719209-161720459	H1-neurons	neurons:	n/a	n/a
39	MXI1	chr1:161719200-161720480	IMR90	lung:	n/a	n/a
40	RUNX3	chr1:161719202-161720308	GM12878	blood:	n/a	n/a
41	SP2	chr1:161719162-161720304	H1-hESC	embryonic stem cell:	n/a	chr1:161719990-161719999 chr1:161719423-161719446
42	TAF1	chr1:161719158-161720423	PFSK-1	brain:	n/a	n/a
43	TAF1	chr1:161719195-161719916	GM12878	blood:	n/a	n/a
44	REST	chr1:161718750-161720601	H1-neurons	neurons:	n/a	chr1:161720166-161720179
45	POLR2A	chr1:161719192-161720442	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr1:161719068-161720695	SK-N-MC	brain:	n/a	n/a
47	YY1	chr1:161719197-161720195	GM12878	blood:	n/a	n/a
48	NR2F2	chr1:161719179-161720241	MCF-7	breast:	n/a	n/a
49	MYBL2	chr1:161719202-161719770	HepG2	liver:	n/a	n/a
50	ARID3A	chr1:161719147-161719739	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161718394..161721019-chr17:57915124..57916843,2	MCF-7	breast:
2	chr1:161719154..161719824-chr10:97849699..97850320,2	Hela-S3	cervix:
3	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:
4	chr1:161703503..161707776-chr1:161717836..161724077,7	K562	blood:
5	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
6	chr1:161718380..161719915-chr8:144772917..144775501,2	MCF-7	breast:
7	chr1:161719167..161719902-chr6:26124018..26124853,2	Hela-S3	cervix:
8	chr1:161694367..161698874-chr1:161718174..161721030,6	MCF-7	breast:
9	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
10	chr1:161718255..161719858-chr8:127569641..127571490,2	MCF-7	breast:
11	chr1:161718427..161720383-chr1:161735445..161737521,2	MCF-7	breast:
12	chr1:161704696..161707209-chr1:161718366..161721899,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FCGR3B-7	chr1:161718366-161719580	NONHSAT007202

No data

Variant related genes	Relation type
DUSP12	TF binding region
ENSG00000226688	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000254286	Chromatin interaction
ENSG00000162746	Chromatin interaction
ENSG00000226889	Chromatin interaction
ENSG00000241347	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000168672	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000181135	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1027702	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs1063178	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10917821	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12121500	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12121522	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs12130299	0.86[CHB][hapmap]
rs12745240	0.94[ASW][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1340981	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs1417580	0.82[GIH][hapmap]
rs16852851	0.89[YRI][hapmap]
rs2066247	0.82[GIH][hapmap]
rs34963459	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35541527	0.89[YRI][hapmap]
rs3820449	0.86[CHB][hapmap]
rs4532807	0.85[YRI][hapmap]
rs4656332	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4657096	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs6427625	0.81[EUR][1000 genomes]
rs6427626	0.82[GIH][hapmap]
rs71634909	0.86[AFR][1000 genomes]
rs953301	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12121310	C1orf61	cis	cerebellum	SCAN
rs12121310	FCRL1	cis	cerebellum	SCAN
rs12121310	PEAR1	cis	parietal	SCAN
rs12121310	ARHGEF11	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161717600-161719400	Weak transcription	Lung	lung
2	chr1:161718600-161720200	Active TSS	Fetal Brain Male	brain
3	chr1:161718800-161719400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr1:161718800-161719400	Flanking Active TSS	Dnd41	blood
5	chr1:161718800-161719400	Flanking Active TSS	Hela-S3	cervix
6	chr1:161718800-161719600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:161718800-161720200	Active TSS	Brain Angular Gyrus	brain
8	chr1:161718800-161720800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr1:161719000-161719400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:161719000-161719400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:161719000-161719400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:161719000-161719400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:161719000-161719400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:161719000-161719400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr1:161719000-161719400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:161719000-161719400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:161719000-161719400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr1:161719000-161719400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr1:161719000-161719400	Active TSS	Brain Germinal Matrix	brain
20	chr1:161719000-161719400	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr1:161719000-161719400	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr1:161719000-161719400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:161719000-161719400	Flanking Active TSS	HUVEC	blood vessel
24	chr1:161719000-161719400	Flanking Active TSS	K562	blood
25	chr1:161719000-161719400	Flanking Active TSS	NHEK	skin
26	chr1:161719000-161719400	Flanking Active TSS	Osteobl	bone
27	chr1:161719000-161719600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr1:161719000-161719600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:161719000-161719800	Active TSS	Fetal Brain Female	brain
30	chr1:161719000-161720000	Active TSS	Primary T cells fromperipheralblood	blood
31	chr1:161719000-161720200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:161719000-161720200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:161719000-161720200	Active TSS	Brain Hippocampus Middle	brain
34	chr1:161719000-161720200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:161719000-161720200	Active TSS	Stomach Smooth Muscle	stomach
36	chr1:161719000-161720400	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr1:161719000-161720400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:161719000-161720600	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr1:161719000-161720800	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr1:161719000-161721000	Active TSS	Right Ventricle	heart
41	chr1:161719200-161719400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:161719200-161719400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr1:161719200-161719400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:161719200-161719400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr1:161719200-161719400	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr1:161719200-161719400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr1:161719200-161719400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:161719200-161719400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:161719200-161719400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr1:161719200-161719400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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