Variant report

Variant	rs11574428
Chromosome Location	chr3:46446721-46446722
allele	A/T
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	chr3:46446612-46446721	K562	blood:	n/a	n/a
2	TBL1XR1	chr3:46446621-46446853	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46435557..46438302-chr3:46445017..46447658,3	MCF-7	breast:
2	chr3:46441114..46442760-chr3:46445695..46448198,2	MCF-7	breast:

Variant related genes	Relation type
CCRL2	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1140865	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574434	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574435	0.84[EUR][1000 genomes]
rs11575821	0.96[EUR][1000 genomes]
rs2157061	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2157062	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2856758	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3092960	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3136535	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34291293	0.95[EUR][1000 genomes]
rs34445878	0.96[EUR][1000 genomes]
rs34971514	0.95[EUR][1000 genomes]
rs35388950	0.95[EUR][1000 genomes]
rs41490645	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4452362	0.83[EUR][1000 genomes]
rs4453882	0.81[EUR][1000 genomes]
rs57093591	0.87[EUR][1000 genomes]
rs6441977	1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap]
rs6762266	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6770674	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6782522	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787972	0.98[EUR][1000 genomes]
rs6791599	1.00[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs6791789	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6798291	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808835	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs762790	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7652037	0.96[EUR][1000 genomes]
rs916093	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs916094	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription 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 target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11574428	ALS2CL	cis	cerebellum	SCAN
rs11574428	ALS2CL	cis	parietal	SCAN
rs11574428	CCR5	trans	multi-tissue	Pritchard
rs11574428	ABHD5	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46428000-46448400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:46437200-46446800	Weak transcription	Hela-S3	cervix
3	chr3:46438600-46447000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:46438800-46447200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:46438800-46459800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:46439200-46448200	Weak transcription	Left Ventricle	heart
7	chr3:46439600-46448400	Weak transcription	Psoas Muscle	Psoas
8	chr3:46442400-46446800	Weak transcription	Fetal Heart	heart
9	chr3:46442400-46447200	Weak transcription	HSMM	muscle
10	chr3:46442400-46448400	Weak transcription	HSMMtube	muscle
11	chr3:46442600-46448200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:46442800-46446800	Weak transcription	NHLF	lung
13	chr3:46443200-46447000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:46443200-46448400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:46445000-46448200	Enhancers	Fetal Intestine Large	intestine
16	chr3:46445000-46448600	Enhancers	Fetal Intestine Small	intestine
17	chr3:46445000-46450000	Enhancers	Spleen	Spleen
18	chr3:46445400-46447000	Weak transcription	Gastric	stomach
19	chr3:46445800-46448600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:46446000-46448600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:46446200-46447000	Enhancers	Adipose Nuclei	Adipose
22	chr3:46446200-46447000	Enhancers	Colonic Mucosa	Colon
23	chr3:46446200-46447600	Enhancers	Ovary	ovary
24	chr3:46446200-46448200	Enhancers	K562	blood
25	chr3:46446200-46448400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr3:46446200-46448600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr3:46446200-46448600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr3:46446200-46448600	Enhancers	Right Atrium	heart
29	chr3:46446200-46450200	Enhancers	Fetal Lung	lung
30	chr3:46446400-46446800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr3:46446400-46447000	Enhancers	Fetal Kidney	kidney
32	chr3:46446400-46447200	Flanking Active TSS	Stomach Mucosa	stomach
33	chr3:46446400-46447400	Weak transcription	Lung	lung
34	chr3:46446400-46447600	Enhancers	Liver	Liver
35	chr3:46446400-46447600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr3:46446400-46447800	Weak transcription	Fetal Thymus	thymus
37	chr3:46446400-46447800	Weak transcription	Small Intestine	intestine
38	chr3:46446400-46448600	Enhancers	Primary B cells from cord blood	blood
39	chr3:46446400-46448600	Enhancers	Placenta	Placenta
40	chr3:46446400-46448600	Enhancers	HUVEC	blood vessel
41	chr3:46446400-46448800	Enhancers	Primary hematopoietic stem cells	blood
42	chr3:46446400-46448800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr3:46446600-46446800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:46446600-46446800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:46446600-46447200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:46446600-46447400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:46446600-46448600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr3:46446600-46448600	Enhancers	Sigmoid Colon	Sigmoid Colon

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