Variant report

Variant	rs41429652
Chromosome Location	chr11:74971747-74971748
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	chr11:74971325-74972240	MCF-7	breast:	n/a	n/a
2	FOSL2	chr11:74971509-74976382	HepG2	liver:	n/a	chr11:74971577-74971585 chr11:74974928-74974935 chr11:74975559-74975566 chr11:74973312-74973323
3	POLR2A	chr11:74971115-74972696	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr11:74970659-74972996	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:74970982-74972170	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:74970579-74972116	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr11:74970661-74975531	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr11:74970875-74972269	Hela-S3	cervix:	n/a	n/a
9	CHD2	chr11:74971478-74971748	K562	blood:	n/a	n/a
10	POLR2A	chr11:74970751-74976821	K562	blood:	n/a	n/a
11	POLR2A	chr11:74971569-74971859	A549	lung:	n/a	n/a
12	POLR2A	chr11:74970936-74976112	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr11:74971481-74976215	HL-60	blood:	n/a	n/a
14	POLR2A	chr11:74971157-74973121	HUVEC	blood vessel:	n/a	n/a
15	SIN3AK20	chr11:74970845-74971875	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr11:74971648-74971872	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:74970589-74976993	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr11:74971182-74976570	HL-60	blood:	n/a	n/a
19	POLR2A	chr11:74971304-74971818	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr11:74970752-74976811	K562	blood:	n/a	n/a
21	POLR2A	chr11:74970887-74974659	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74959514..74960333-chr11:74971667..74972528,2	MCF-7	breast:
2	chr11:74699676..74701249-chr11:74971380..74973651,2	K562	blood:
3	chr11:74971389..74975056-chr11:74976181..74978822,5	K562	blood:

Variant related genes	Relation type
ENSG00000254963	TF binding region
ENSG00000162139	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12721493	1.00[AMR][1000 genomes]
rs34931451	1.00[AMR][1000 genomes]
rs55977292	1.00[AMR][1000 genomes]
rs56709079	1.00[AMR][1000 genomes]
rs59496705	1.00[AMR][1000 genomes]
rs60313751	1.00[AMR][1000 genomes]
rs60585327	1.00[AMR][1000 genomes]
rs61324508	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv1049887	chr11:74937977-75040438	Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1036292	chr11:74937977-75059496	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1041640	chr11:74945824-75174688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
4	nsv832211	chr11:74945839-75106125	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41429652	PPP4R4	trans	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74969200-74976600	Weak transcription	Ovary	ovary
2	chr11:74969400-74972000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr11:74969800-74972000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr11:74969800-74973800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr11:74969800-74976000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:74969800-74976000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr11:74969800-74976200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr11:74970000-74976000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr11:74970600-74973000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:74970600-74973200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:74970600-74975000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:74970600-74975400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr11:74970600-74975800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:74970800-74972200	Enhancers	Fetal Stomach	stomach
15	chr11:74970800-74972600	Enhancers	Brain Angular Gyrus	brain
16	chr11:74970800-74973000	Enhancers	Right Ventricle	heart
17	chr11:74970800-74973200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:74970800-74973200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:74970800-74973200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr11:74970800-74975800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:74970800-74988200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr11:74971000-74971800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr11:74971000-74972400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:74971000-74972600	Enhancers	Brain Cingulate Gyrus	brain
25	chr11:74971000-74972600	Enhancers	Fetal Thymus	thymus
26	chr11:74971000-74972800	Enhancers	Brain Substantia Nigra	brain
27	chr11:74971000-74972800	Enhancers	Right Atrium	heart
28	chr11:74971000-74973400	Enhancers	Primary T cells from cord blood	blood
29	chr11:74971000-74973600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr11:74971000-74974600	Enhancers	Stomach Smooth Muscle	stomach
31	chr11:74971200-74973200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr11:74971200-74975200	Weak transcription	Fetal Intestine Small	intestine
33	chr11:74971200-74975800	Enhancers	Adipose Nuclei	Adipose
34	chr11:74971200-74976200	Enhancers	Primary hematopoietic stem cells	blood
35	chr11:74971400-74972000	Enhancers	Brain Anterior Caudate	brain
36	chr11:74971400-74972000	Enhancers	Fetal Brain Female	brain
37	chr11:74971400-74972000	Enhancers	Fetal Lung	lung
38	chr11:74971400-74972200	Enhancers	Fetal Muscle Trunk	muscle
39	chr11:74971400-74972600	Enhancers	Brain Hippocampus Middle	brain
40	chr11:74971400-74972600	Enhancers	Duodenum Mucosa	Duodenum
41	chr11:74971400-74972800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr11:74971400-74972800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr11:74971400-74973200	Enhancers	Left Ventricle	heart
44	chr11:74971400-74974200	Enhancers	Spleen	Spleen
45	chr11:74971400-74974600	Enhancers	Lung	lung
46	chr11:74971400-74977800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr11:74971600-74971800	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr11:74971600-74972000	Enhancers	Fetal Muscle Leg	muscle
49	chr11:74971600-74972000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr11:74971600-74972200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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