Variant report

Variant	rs2004649
Chromosome Location	chr11:65380916-65380917
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	chr11:65380118-65382306	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr11:65380316-65385264	GM12892	blood:	n/a	n/a
3	EGR1	chr11:65380864-65382142	HCT-116	colon:	n/a	chr11:65381416-65381440 chr11:65381728-65381742 chr11:65381727-65381740 chr11:65381282-65381295 chr11:65381283-65381292
4	MAX	chr11:65380738-65382169	MCF-7	breast:	n/a	n/a
5	POLR2A	chr11:65380366-65381147	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:65380725-65381074	HUVEC	blood vessel:	n/a	n/a
7	EGR1	chr11:65380910-65381384	K562	blood:	n/a	chr11:65381282-65381295 chr11:65381283-65381292
8	POLR2A	chr11:65380652-65384148	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr11:65380340-65381109	HepG2	liver:	n/a	n/a
10	MAZ	chr11:65380699-65382214	IMR90	lung:	n/a	n/a
11	POLR2A	chr11:65380376-65381126	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:65380575-65381043	HepG2	liver:	n/a	n/a
13	POLR2A	chr11:65380014-65384391	K562	blood:	n/a	n/a
14	POLR2A	chr11:65380460-65381164	GM12892	blood:	n/a	n/a
15	POLR2A	chr11:65380301-65383670	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr11:65380865-65381018	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr11:65380283-65385739	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:65380432-65382548	MCF-7	breast:	n/a	n/a
19	POLR2A	chr11:65380335-65381076	HepG2	liver:	n/a	n/a
20	STAT5A	chr11:65380641-65380929	GM12878	blood:	n/a	n/a
21	MXI1	chr11:65380336-65384590	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr11:65379608-65384450	HepG2	liver:	n/a	n/a
23	EGR1	chr11:65380842-65381916	K562	blood:	n/a	chr11:65381416-65381440 chr11:65381728-65381742 chr11:65381727-65381740 chr11:65381282-65381295 chr11:65381283-65381292
24	CHD1	chr11:65380475-65384275	IMR90	lung:	n/a	chr11:65382884-65382894
25	MYC	chr11:65380864-65381098	MCF-7	breast:	n/a	n/a
26	EGR1	chr11:65380898-65382032	MCF-7	breast:	n/a	chr11:65381416-65381440 chr11:65381728-65381742 chr11:65381727-65381740 chr11:65381282-65381295 chr11:65381283-65381292
27	POLR2A	chr11:65380614-65381199	GM12892	blood:	n/a	n/a
28	POLR2A	chr11:65380830-65381017	GM12878	blood:	n/a	n/a
29	POLR2A	chr11:65380267-65382207	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65306623..65309907-chr11:65380382..65384254,6	MCF-7	breast:
2	chr11:65380696..65385200-chr11:65403578..65408941,10	MCF-7	breast:
3	chr11:65336061..65346997-chr11:65371025..65390625,42	MCF-7	breast:
4	chr11:65335401..65344755-chr11:65379602..65385163,20	K562	blood:
5	chr11:65379507..65381898-chr11:65478593..65480836,3	MCF-7	breast:
6	chr11:65377447..65384699-chr11:65622853..65629192,15	MCF-7	breast:
7	chr11:65380332..65382692-chr11:65425044..65427777,2	MCF-7	breast:
8	chr11:65380602..65383246-chr11:65768678..65771455,2	K562	blood:
9	chr11:65313091..65315677-chr11:65380016..65384543,4	K562	blood:
10	chr11:65379754..65386537-chr11:65415130..65425067,26	MCF-7	breast:
11	chr11:65380590..65383285-chr11:118661411..118663199,3	MCF-7	breast:
12	chr11:65264270..65268654-chr11:65380562..65385771,6	K562	blood:
13	chr11:65362693..65364278-chr11:65379857..65381562,2	MCF-7	breast:
14	chr11:65189868..65193892-chr11:65380372..65385774,5	MCF-7	breast:
15	chr11:65186294..65191468-chr11:65379126..65384544,8	MCF-7	breast:
16	chr11:65379382..65381095-chr17:60730050..60732492,2	MCF-7	breast:

Variant related genes	Relation type
MAP3K11	TF binding region
PCNXL3	TF binding region
ENSG00000172732	Chromatin interaction
ENSG00000265874	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000260233	Chromatin interaction
ENSG00000176973	Chromatin interaction
ENSG00000173338	Chromatin interaction
ENSG00000266041	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000110367	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000213445	Chromatin interaction
ENSG00000251562	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11227241	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1144789	0.85[CEU][hapmap];0.97[GIH][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1151490	0.85[CEU][hapmap];0.97[GIH][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61744384	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7116712	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.87[ASN][1000 genomes]
rs7130955	0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	1003 gene(s)	inside rSNPs	diseases
4	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
5	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
6	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
7	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
8	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
10	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
11	nsv468599	chr11:65335705-65427346	ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
12	nsv555213	chr11:65335705-65427346	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
13	nsv897732	chr11:65335705-65427346	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
14	nsv468600	chr11:65335705-65431360	Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
15	nsv555214	chr11:65335705-65431360	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
16	nsv897733	chr11:65335705-65431360	Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
17	nsv897734	chr11:65335705-65436888	Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
18	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats 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 miRNA target site	98 gene(s)	inside rSNPs	diseases
19	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers 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	227 gene(s)	inside rSNPs	diseases
20	nsv897739	chr11:65337714-65388300	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
21	nsv897743	chr11:65338589-65382564	Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
22	esv2761680	chr11:65344328-65391317	Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	46 gene(s)	inside rSNPs	diseases
23	nsv897746	chr11:65349756-65427346	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
24	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2004649	MAP3K11	cis	lung	GTEx
rs2004649	MAP3K11	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65376600-65381000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:65376800-65381800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:65377400-65381000	Flanking Active TSS	HUVEC	blood vessel
4	chr11:65378000-65381000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:65378000-65381200	Enhancers	Fetal Heart	heart
6	chr11:65378000-65381600	Enhancers	Fetal Brain Male	brain
7	chr11:65378000-65381800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr11:65378200-65381000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr11:65378200-65381200	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr11:65378200-65381400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
11	chr11:65378200-65382800	Active TSS	Right Atrium	heart
12	chr11:65378400-65381000	Flanking Active TSS	NH-A	brain
13	chr11:65378400-65384200	Active TSS	Psoas Muscle	Psoas
14	chr11:65378600-65381000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr11:65378600-65381200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr11:65378600-65381200	Flanking Active TSS	Liver	Liver
17	chr11:65378800-65381000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr11:65378800-65381000	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr11:65378800-65381600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr11:65378800-65384000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr11:65379000-65381200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:65379000-65384400	Active TSS	Fetal Kidney	kidney
23	chr11:65379200-65381000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:65379400-65381000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:65379400-65381000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:65379400-65381000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:65379400-65381000	Flanking Active TSS	HSMM	muscle
28	chr11:65379400-65381000	Flanking Active TSS	Osteobl	bone
29	chr11:65379600-65381000	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr11:65379600-65381000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr11:65379600-65381000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr11:65379600-65381000	Transcr. at gene 5' and 3'	Placenta	Placenta
33	chr11:65379800-65384000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr11:65380000-65381000	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
35	chr11:65380000-65381000	Flanking Active TSS	Gastric	stomach
36	chr11:65380000-65381000	Flanking Active TSS	Left Ventricle	heart
37	chr11:65380000-65381200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:65380000-65381200	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr11:65380000-65381200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr11:65380000-65382000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr11:65380200-65381000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:65380200-65381000	Flanking Active TSS	Colonic Mucosa	Colon
43	chr11:65380200-65381000	Flanking Active TSS	HSMMtube	muscle
44	chr11:65380200-65381200	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr11:65380200-65381400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr11:65380200-65384600	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr11:65380400-65381000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:65380400-65381000	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr11:65380400-65381000	Flanking Active TSS	Colon Smooth Muscle	Colon
50	chr11:65380400-65381000	Flanking Active TSS	Esophagus	oesophagus

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