Variant report

Variant	rs1391980
Chromosome Location	chr4:129218126-129218127
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129216692..129219211-chr4:129248139..129251000,2	MCF-7	breast:
2	chr4:129215263..129217433-chr4:129217570..129219858,4	K562	blood:
3	chr4:129215849..129218784-chr4:129229247..129231536,2	K562	blood:
4	chr4:129215061..129219727-chr4:129220419..129226220,7	K562	blood:
5	chr4:129211991..129214789-chr4:129216547..129219460,2	K562	blood:
6	chr4:129208338..129210994-chr4:129216298..129218698,3	K562	blood:

Variant related genes	Relation type
ENSG00000164040	Chromatin interaction
ENSG00000251432	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11098953	0.80[ASN][1000 genomes]
rs11098954	0.80[ASN][1000 genomes]
rs11728141	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12505763	0.96[CEU][hapmap];0.89[GIH][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs12650034	0.92[ASN][1000 genomes]
rs13103317	0.91[ASN][1000 genomes]
rs1829726	0.91[ASN][1000 genomes]
rs1851399	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2036687	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2101808	0.91[ASN][1000 genomes]
rs2202805	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2391257	0.92[ASN][1000 genomes]
rs28609279	0.81[ASN][1000 genomes]
rs3755896	0.92[ASN][1000 genomes]
rs4016	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs430431	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4975180	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs60515985	0.97[EUR][1000 genomes]
rs62318161	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6814132	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6816625	0.81[ASN][1000 genomes]
rs6842987	0.92[ASN][1000 genomes]
rs6849992	0.81[ASN][1000 genomes]
rs7666566	0.92[ASN][1000 genomes]
rs9790593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1391980	HSPA4L	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129210000-129224400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:129210200-129228600	Weak transcription	Left Ventricle	heart
3	chr4:129210200-129230400	Weak transcription	Ovary	ovary
4	chr4:129210200-129245800	Weak transcription	Esophagus	oesophagus
5	chr4:129210400-129218600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:129210400-129222400	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:129210400-129226200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:129210400-129227200	Weak transcription	Pancreas	Pancrea
9	chr4:129210400-129227800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:129210400-129231000	Weak transcription	HSMMtube	muscle
11	chr4:129210400-129231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:129210400-129235800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:129210400-129238000	Weak transcription	Thymus	Thymus
14	chr4:129210400-129240000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:129210400-129246400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:129210400-129247600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:129210600-129222800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:129210600-129231000	Weak transcription	Osteobl	bone
19	chr4:129210600-129249800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:129210800-129219400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:129210800-129221200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:129210800-129226400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:129210800-129227800	Weak transcription	Fetal Brain Male	brain
24	chr4:129210800-129230400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:129210800-129233000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:129211000-129218600	Weak transcription	Primary T cells from cord blood	blood
27	chr4:129211000-129226200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:129211000-129231000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:129211000-129244200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:129211000-129246400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:129211200-129220000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:129211200-129223400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:129211200-129231200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr4:129211200-129244000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:129211200-129248200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr4:129211200-129254400	Weak transcription	Brain Substantia Nigra	brain
37	chr4:129211400-129228200	Weak transcription	GM12878-XiMat	blood
38	chr4:129211400-129228600	Weak transcription	Small Intestine	intestine
39	chr4:129211400-129231200	Weak transcription	A549	lung
40	chr4:129213800-129226400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:129214400-129218400	Weak transcription	Liver	Liver
42	chr4:129216000-129222200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:129216000-129222200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:129216600-129231400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:129216800-129228400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:129216800-129228600	Weak transcription	Gastric	stomach
47	chr4:129217000-129218400	Weak transcription	Stomach Mucosa	stomach
48	chr4:129217000-129218600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:129217000-129219200	Weak transcription	K562	blood
50	chr4:129217000-129223400	Weak transcription	Adipose Nuclei	Adipose

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