Variant report

Variant	rs3733415
Chromosome Location	chr4:187630590-187630591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:187629081..187631541-chr4:187646256..187647972,2	MCF-7	breast:
2	chr4:187628920..187631619-chr4:187637176..187639413,2	K562	blood:

Variant related genes	Relation type
ENSG00000083857	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17077740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017933	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs327067	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs327093	0.82[EUR][1000 genomes]
rs327095	0.88[GIH][hapmap]
rs327100	0.84[EUR][1000 genomes]
rs327101	0.90[GIH][hapmap]
rs327102	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs327111	0.82[CHB][hapmap]
rs3733409	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs455219	0.95[GIH][hapmap]
rs462509	0.82[CHB][hapmap]
rs59035714	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818461	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73015642	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73015656	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73015660	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73015670	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025088	chr4:187407683-187674585	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1025244	chr4:187419770-188284813	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1034212	chr4:187437895-188030805	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv537438	chr4:187437895-188030805	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv532745	chr4:187471692-188205443	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv1022262	chr4:187475862-187848284	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1024705	chr4:187534005-187849091	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1026970	chr4:187537418-187913351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv596440	chr4:187538133-187848075	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3733415	HELT	cis	parietal	SCAN
rs3733415	CLDN22	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187608000-187632400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:187622600-187634200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:187623200-187631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:187623200-187632000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:187623400-187632800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:187623800-187631600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:187624000-187632000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:187624400-187631000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:187624800-187633800	Weak transcription	Brain Substantia Nigra	brain
10	chr4:187625000-187631800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:187625400-187631000	Strong transcription	HMEC	breast
12	chr4:187625800-187630800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:187625800-187631000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:187626200-187631000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:187626200-187631000	Strong transcription	Fetal Intestine Large	intestine
16	chr4:187626200-187631000	Strong transcription	NH-A	brain
17	chr4:187626400-187630800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:187626400-187631000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:187626400-187631000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:187626400-187631000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:187626400-187631000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:187626400-187631200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:187626400-187631200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:187626400-187643600	Weak transcription	Stomach Mucosa	stomach
25	chr4:187626600-187630600	Strong transcription	Fetal Lung	lung
26	chr4:187626600-187630600	Strong transcription	Fetal Stomach	stomach
27	chr4:187626600-187630800	Strong transcription	HSMMtube	muscle
28	chr4:187626600-187631000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:187626600-187631000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr4:187626600-187631000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:187626600-187631000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:187626600-187631000	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr4:187626600-187631000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:187626600-187631000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr4:187626600-187631000	Strong transcription	NHDF-Ad	bronchial
36	chr4:187626600-187631000	Strong transcription	NHLF	lung
37	chr4:187626600-187631000	Strong transcription	Osteobl	bone
38	chr4:187626600-187632200	Strong transcription	NHEK	skin
39	chr4:187626800-187630600	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr4:187626800-187630600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:187626800-187631000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:187626800-187631000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:187626800-187631000	Strong transcription	A549	lung
44	chr4:187627000-187630800	Strong transcription	Fetal Muscle Leg	muscle
45	chr4:187627000-187631000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:187627000-187631400	Strong transcription	HSMM	muscle
47	chr4:187627200-187631000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:187627400-187631400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:187627400-187631600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:187627600-187631200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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