Variant report

Variant	rs4910858
Chromosome Location	chr11:3875411-3875412
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	RELA	chr11:3875089-3876771	GM10847	blood:	n/a	n/a
2	POLR2A	chr11:3875307-3876592	GM12892	blood:	n/a	n/a
3	NFIC	chr11:3875105-3876559	GM12878	blood:	n/a	n/a
4	SPI1	chr11:3875203-3875520	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:3875304-3877670	GM19099	blood:	n/a	n/a
6	POLR2A	chr11:3875197-3876762	GM12878	blood:	n/a	n/a
7	SPI1	chr11:3875177-3875982	GM12891	blood:	n/a	n/a
8	CHD1	chr11:3875301-3876848	IMR90	lung:	n/a	n/a
9	MYC	chr11:3875130-3878021	K562	blood:	n/a	chr11:3877019-3877029 chr11:3876969-3876979
10	RCOR1	chr11:3874971-3876804	GM12878	blood:	n/a	n/a
11	RELA	chr11:3875154-3876639	GM18951	blood:	n/a	n/a
12	RELA	chr11:3875296-3876779	GM15510	blood:	n/a	n/a
13	CREB1	chr11:3875245-3876669	GM12878	blood:	n/a	n/a
14	RUNX3	chr11:3875081-3876862	GM12878	blood:	n/a	n/a
15	POLR2A	chr11:3875132-3876771	GM12892	blood:	n/a	n/a
16	TBL1XR1	chr11:3875216-3875884	K562	blood:	n/a	n/a
17	TAL1	chr11:3875270-3875422	K562	blood:	n/a	n/a
18	CHD2	chr11:3875190-3876732	GM12878	blood:	n/a	n/a
19	CHD2	chr11:3875131-3875751	K562	blood:	n/a	n/a
20	RELA	chr11:3875370-3876786	GM12891	blood:	n/a	n/a
21	POLR2A	chr11:3875249-3877806	Raji	blood:	n/a	n/a
22	POLR2A	chr11:3875275-3876570	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:3875338-3877677	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:3875370-3877709	GM18505	blood:	n/a	n/a
25	JUND	chr11:3874713-3876949	K562	blood:	n/a	chr11:3876024-3876033
26	POLR2A	chr11:3875327-3877709	K562	blood:	n/a	n/a
27	POLR2A	chr11:3875358-3876137	GM12891	blood:	n/a	n/a
28	SPI1	chr11:3875276-3876157	GM12878	blood:	n/a	n/a
29	TBP	chr11:3875003-3876592	GM12878	blood:	n/a	n/a
30	IRF1	chr11:3875028-3875876	K562	blood:	n/a	n/a
31	POLR2A	chr11:3875252-3877125	GM12891	blood:	n/a	n/a
32	MAZ	chr11:3875401-3878133	GM12878	blood:	n/a	chr11:3877019-3877029 chr11:3876969-3876979
33	RUNX3	chr11:3875140-3876812	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:3875159-3876844	GM12892	blood:	n/a	n/a
35	TBL1XR1	chr11:3875294-3876706	GM12878	blood:	n/a	n/a
36	POU2F2	chr11:3875143-3876667	GM12878	blood:	n/a	chr11:3876107-3876120
37	ATF2	chr11:3875155-3876536	GM12878	blood:	n/a	n/a
38	RELA	chr11:3875318-3876792	GM19099	blood:	n/a	n/a
39	POLR2A	chr11:3875354-3877678	GM12892	blood:	n/a	n/a
40	CBX3	chr11:3874688-3876683	K562	blood:	n/a	n/a
41	MTA3	chr11:3875293-3876257	GM12878	blood:	n/a	n/a
42	RCOR1	chr11:3874962-3875418	K562	blood:	n/a	n/a
43	POLR2A	chr11:3875384-3877726	GM19193	blood:	n/a	n/a
44	EP300	chr11:3875191-3876818	GM12878	blood:	n/a	n/a
45	PAX5	chr11:3875177-3876755	GM12878	blood:	n/a	n/a
46	JUN	chr11:3874671-3876807	K562	blood:	n/a	chr11:3876024-3876033
47	ZNF143	chr11:3875274-3875525	K562	blood:	n/a	n/a
48	POLR2A	chr11:3875376-3876813	GM12878	blood:	n/a	n/a
49	POLR2A	chr11:3875258-3876696	GM12892	blood:	n/a	n/a
50	EBF1	chr11:3875294-3876496	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:3858623..3864245-chr11:3874959..3879217,11	K562	blood:
2	chr11:3861261..3864016-chr11:3874431..3876289,3	MCF-7	breast:
3	chr11:3860189..3865275-chr11:3872883..3879283,10	K562	blood:

Variant related genes	Relation type
ENSG00000229368	TF binding region
STIM1	TF binding region
MIR4687	TF binding region
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10835184	0.80[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10835185	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10835191	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835192	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11030054	0.96[ASN][1000 genomes]
rs12278324	0.85[ASN][1000 genomes]
rs12417801	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12421093	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12795081	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1869002	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813879	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3813880	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7131058	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1046325	chr11:3856201-3895148	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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	16 gene(s)	inside rSNPs	diseases
9	nsv1039059	chr11:3856201-3909415	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv540910	chr11:3856201-3909415	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
13	nsv896894	chr11:3859856-3888234	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4910858	PGAP2	cis	brain	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3867000-3875600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:3870600-3875600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:3871000-3875600	Weak transcription	A549	lung
4	chr11:3872800-3875600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr11:3873800-3875800	Enhancers	Primary hematopoietic stem cells	blood
6	chr11:3874000-3875600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr11:3874000-3875600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:3874200-3876400	Weak transcription	Small Intestine	intestine
9	chr11:3874400-3875600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:3874600-3875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:3874600-3875800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:3874600-3876200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr11:3874800-3875800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr11:3874800-3876000	Enhancers	Fetal Muscle Leg	muscle
15	chr11:3874800-3876200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr11:3875000-3875600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr11:3875000-3875600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr11:3875000-3875600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:3875000-3875600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr11:3875000-3876000	Weak transcription	Psoas Muscle	Psoas
21	chr11:3875000-3876200	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr11:3875000-3876200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr11:3875000-3876200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr11:3875000-3876200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr11:3875200-3875600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr11:3875200-3875600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:3875200-3875600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr11:3875200-3875600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:3875200-3875600	Enhancers	Adipose Nuclei	Adipose
30	chr11:3875200-3875600	Enhancers	Duodenum Mucosa	Duodenum
31	chr11:3875200-3875800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr11:3875200-3875800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr11:3875200-3875800	Enhancers	Brain Anterior Caudate	brain
34	chr11:3875200-3875800	Enhancers	Brain Hippocampus Middle	brain
35	chr11:3875200-3875800	Enhancers	Hela-S3	cervix
36	chr11:3875200-3875800	Enhancers	HMEC	breast
37	chr11:3875200-3876000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:3875200-3876000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:3875200-3876000	Enhancers	Fetal Intestine Small	intestine
40	chr11:3875200-3876000	Enhancers	Pancreas	Pancrea
41	chr11:3875200-3876000	Enhancers	Spleen	Spleen
42	chr11:3875200-3876200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:3875200-3876200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:3875200-3876200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:3875200-3876200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr11:3875200-3876200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:3875200-3876200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr11:3875200-3876200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr11:3875200-3876200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr11:3875200-3876200	Enhancers	Placenta	Placenta

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