Variant report

Variant	rs1891705
Chromosome Location	chr1:112938497-112938498
allele	C/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	PAX5	chr1:112938481-112938638	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:112938334-112939103	Hela-S3	cervix:	n/a	n/a
3	RCOR1	chr1:112938415-112939062	K562	blood:	n/a	n/a
4	TAF1	chr1:112938446-112939165	H1-neurons	neurons:	n/a	n/a
5	BACH1	chr1:112938444-112938601	K562	blood:	n/a	n/a
6	GABPA	chr1:112938309-112939044	SK-N-SH	brain:	n/a	chr1:112939019-112939028
7	GABPA	chr1:112938489-112938734	Hela-S3	cervix:	n/a	n/a
8	CREB1	chr1:112938237-112939088	HepG2	liver:	n/a	n/a
9	MAX	chr1:112938389-112939002	A549	lung:	n/a	n/a
10	POLR2A	chr1:112938385-112939125	HCT-116	colon:	n/a	n/a
11	NFYA	chr1:112938091-112939177	Hela-S3	cervix:	n/a	n/a
12	TAF1	chr1:112938450-112939002	HepG2	liver:	n/a	n/a
13	SP1	chr1:112938419-112939054	H1-hESC	embryonic stem cell:	n/a	chr1:112939020-112939029 chr1:112938726-112938738 chr1:112938821-112938833 chr1:112939019-112939029 chr1:112939020-112939029 chr1:112939018-112939030 chr1:112938727-112938736 chr1:112938821-112938833 chr1:112939018-112939030 chr1:112938728-112938737 chr1:112939019-112939029 chr1:112938818-112938832 chr1:112938822-112938831 chr1:112938727-112938741 chr1:112938823-112938832 chr1:112938726-112938737 chr1:112939019-112939028 chr1:112939015-112939029
14	RCOR1	chr1:112937996-112939603	Hela-S3	cervix:	n/a	n/a
15	NFYA	chr1:112938285-112939153	K562	blood:	n/a	n/a
16	PAX5	chr1:112938393-112938795	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:112938449-112939121	Gliobla	brain:	n/a	n/a
18	CHD2	chr1:112938431-112939603	GM12878	blood:	n/a	n/a
19	ZNF143	chr1:112938469-112938852	K562	blood:	n/a	n/a
20	POLR2A	chr1:112938338-112939881	H1-neurons	neurons:	n/a	n/a
21	SP1	chr1:112938406-112939115	H1-hESC	embryonic stem cell:	n/a	chr1:112939020-112939029 chr1:112938726-112938738 chr1:112938821-112938833 chr1:112939019-112939029 chr1:112939020-112939029 chr1:112939018-112939030 chr1:112938727-112938736 chr1:112938821-112938833 chr1:112939018-112939030 chr1:112938728-112938737 chr1:112939019-112939029 chr1:112938818-112938832 chr1:112938822-112938831 chr1:112938727-112938741 chr1:112938823-112938832 chr1:112938726-112938737 chr1:112939019-112939028 chr1:112939015-112939029
22	POLR2A	chr1:112935622-112939617	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr1:112938371-112939167	ECC-1	luminal epithelium:	n/a	n/a
24	MAZ	chr1:112938328-112939554	K562	blood:	n/a	chr1:112939017-112939027
25	REST	chr1:112938438-112938740	SK-N-SH	brain:	n/a	chr1:112938610-112938630 chr1:112938614-112938627
26	POLR2A	chr1:112938387-112940060	GM19099	blood:	n/a	n/a
27	ZNF143	chr1:112938457-112939264	H1-hESC	embryonic stem cell:	n/a	chr1:112939035-112939053
28	POLR2A	chr1:112938419-112939103	A549	lung:	n/a	n/a
29	HMGN3	chr1:112938484-112939065	K562	blood:	n/a	n/a
30	ZC3H11A	chr1:112938290-112938852	K562	blood:	n/a	n/a
31	CHD2	chr1:112938483-112938993	H1-hESC	embryonic stem cell:	n/a	n/a
32	GABPA	chr1:112938441-112938872	HepG2	liver:	n/a	n/a
33	CREB1	chr1:112938406-112938839	ECC-1	luminal epithelium:	n/a	n/a
34	GABPA	chr1:112938308-112939028	MCF-7	breast:	n/a	chr1:112939019-112939028
35	GABPA	chr1:112938165-112938859	A549	lung:	n/a	n/a
36	MAX	chr1:112938436-112939776	GM12878	blood:	n/a	chr1:112939017-112939027
37	REST	chr1:112938309-112939738	H1-neurons	neurons:	n/a	chr1:112938321-112938331 chr1:112938610-112938630 chr1:112938319-112938339 chr1:112939163-112939176 chr1:112938614-112938627 chr1:112938319-112938333
38	POLR2A	chr1:112938377-112939198	U87	brain:	n/a	n/a
39	MAX	chr1:112938345-112938885	ECC-1	luminal epithelium:	n/a	n/a
40	GTF2F1	chr1:112938497-112939085	Hela-S3	cervix:	n/a	n/a
41	CREB1	chr1:112938338-112939047	HepG2	liver:	n/a	n/a
42	GABPA	chr1:112938458-112938866	K562	blood:	n/a	n/a
43	POLR2A	chr1:112937750-112938974	HepG2	liver:	n/a	n/a
44	POLR2A	chr1:112938015-112939192	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:112938286-112939077	MCF10A-Er-Src	breast:	n/a	n/a
46	ZBTB7A	chr1:112938431-112938653	HepG2	liver:	n/a	n/a
47	JUND	chr1:112938376-112939056	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr1:112938311-112939149	PANC-1	pancreas:	n/a	n/a
49	CREB1	chr1:112938355-112939080	H1-hESC	embryonic stem cell:	n/a	n/a
50	ZNF143	chr1:112938470-112939096	Hela-S3	cervix:	n/a	chr1:112939035-112939053

No.	Distal block	Cell Line	Cell type
1	chr1:112934882..112939118-chr1:113160574..113165273,5	K562	blood:
2	chr1:90285374..90287672-chr1:112937742..112939314,2	MCF-7	breast:
3	chr1:112938137..112939101-chr16:67207540..67208291,2	Hela-S3	cervix:
4	chr1:112937855..112940278-chr1:113239914..113242532,2	MCF-7	breast:
5	chr1:112936058..112938767-chr1:113217023..113219296,3	MCF-7	breast:
6	chr1:112936014..112938715-chr1:113162685..113165273,2	K562	blood:
7	chr1:112936667..112940657-chr1:113004024..113011069,20	MCF-7	breast:
8	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
9	chr1:112935506..112938750-chr1:113247926..113251541,4	MCF-7	breast:
10	chr1:112936910..112939069-chr1:113249610..113251300,2	K562	blood:
11	chr1:112934468..112938679-chr1:113215370..113218926,7	MCF-7	breast:
12	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
13	chr1:112938289..112939065-chr6:26157383..26158365,2	Hela-S3	cervix:
14	chr1:112937187..112939558-chr17:38473517..38475542,2	MCF-7	breast:
15	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
16	chr1:112935548..112944315-chr1:113002393..113010397,28	MCF-7	breast:
17	chr1:112938006..112938734-chr5:90676277..90676835,2	Hela-S3	cervix:

Variant related genes	Relation type
CTTNBP2NL	TF binding region
ENSG00000007341	Chromatin interaction
ENSG00000140939	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000272931	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000171492	Chromatin interaction
ENSG00000158373	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1018712	0.83[CEU][hapmap]
rs11102471	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1177812	0.83[CEU][hapmap]
rs12080074	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138024	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1412931	0.83[CEU][hapmap]
rs1419041	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475710	0.83[CEU][hapmap]
rs1759689	0.83[CEU][hapmap]
rs1759692	0.86[CEU][hapmap]
rs1777608	0.83[CEU][hapmap]
rs1891707	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2483328	0.83[CEU][hapmap]
rs2488758	0.83[CEU][hapmap]
rs2488762	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2488763	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488766	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488769	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488770	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488787	0.83[CEU][hapmap]
rs2492501	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2492502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492503	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492504	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492507	0.82[CEU][hapmap]
rs2492512	0.83[CEU][hapmap]
rs2492513	0.83[CEU][hapmap]
rs2492534	0.83[CEU][hapmap]
rs2999472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240532	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7415832	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7541222	0.83[CEU][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1891705	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112934800-112938600	Flanking Active TSS	HUVEC	blood vessel
2	chr1:112936200-112938600	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr1:112936200-112940000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:112936800-112938600	Flanking Active TSS	HSMMtube	muscle
5	chr1:112937000-112938600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:112937000-112938600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr1:112937000-112938600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:112937000-112938600	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr1:112937000-112938600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr1:112937000-112938600	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr1:112937000-112938600	Flanking Active TSS	Hela-S3	cervix
12	chr1:112937000-112938600	Flanking Active TSS	NH-A	brain
13	chr1:112937000-112938600	Flanking Active TSS	NHEK	skin
14	chr1:112937000-112938600	Flanking Active TSS	NHLF	lung
15	chr1:112937000-112940000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:112937200-112938600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:112937200-112938600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:112937600-112938800	Active TSS	Brain Germinal Matrix	brain
19	chr1:112938000-112938600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:112938000-112938600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:112938000-112938600	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr1:112938000-112938600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr1:112938000-112938600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr1:112938000-112938600	Flanking Active TSS	Liver	Liver
25	chr1:112938000-112938600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:112938000-112938600	Flanking Active TSS	Dnd41	blood
27	chr1:112938000-112938600	Flanking Active TSS	Osteobl	bone
28	chr1:112938000-112938800	Flanking Active TSS	HMEC	breast
29	chr1:112938000-112940000	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr1:112938000-112940000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr1:112938000-112940000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr1:112938000-112941000	Active TSS	Aorta	Aorta
33	chr1:112938200-112938600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr1:112938200-112938600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr1:112938200-112938600	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr1:112938200-112938600	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr1:112938200-112938600	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr1:112938200-112938600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:112938200-112938600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:112938200-112938600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr1:112938200-112938600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr1:112938200-112938600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr1:112938200-112938600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:112938200-112938600	Flanking Active TSS	Placenta	Placenta
45	chr1:112938200-112938600	Flanking Active TSS	HSMM	muscle
46	chr1:112938200-112938600	Flanking Active TSS	K562	blood
47	chr1:112938200-112938800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
48	chr1:112938200-112938800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:112938200-112939000	Active TSS	HepG2	liver
50	chr1:112938200-112939400	Active TSS	Colon Smooth Muscle	Colon

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