Variant report

Variant	rs1421911
Chromosome Location	chr5:96000947-96000948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95995785..95997823-chr5:95999172..96000986,2	K562	blood:
2	chr5:96000243..96001872-chr5:96034533..96037143,2	MCF-7	breast:
3	chr5:95994913..95997156-chr5:96000541..96002076,2	MCF-7	breast:
4	chr5:96000044..96002037-chr5:96005700..96007687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10045215	0.84[ASN][1000 genomes]
rs10067766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10075736	0.84[ASN][1000 genomes]
rs151835	1.00[JPT][hapmap]
rs151904	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs152005	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs152014	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs152017	0.82[JPT][hapmap]
rs152020	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2351245	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs246109	0.84[ASN][1000 genomes]
rs26482	0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs26483	0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs26484	0.85[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs26485	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs26503	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs26504	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs28040	0.91[ASN][1000 genomes]
rs28093	0.86[JPT][hapmap]
rs28104	0.86[JPT][hapmap]
rs31248	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs31249	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs31250	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4267886	0.91[ASN][1000 genomes]
rs4590196	0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6556937	0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6860934	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6897588	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7704167	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7705824	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7733671	0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][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	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS 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	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1421911	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs1421911	CAST	cis	Adipose Subcutaneous	GTEx
rs1421911	CAST	cis	Nerve Tibial	GTEx
rs1421911	CAST	cis	cerebellum	SCAN
rs1421911	CAST	cis	Whole Blood	GTEx
rs1421911	CAST	cis	lung	GTEx
rs1421911	CAST	cis	multi-tissue	Pritchard
rs1421911	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs1421911	CAST	cis	parietal	SCAN
rs1421911	CTC-506B8.1	cis	Whole Blood	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95999400-96001000	Flanking Active TSS	HMEC	breast
2	chr5:95999400-96001400	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr5:95999400-96001600	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr5:95999400-96002000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:95999400-96002600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:95999400-96002800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:95999400-96005000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:95999400-96018200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:95999400-96038000	Weak transcription	Fetal Stomach	stomach
10	chr5:95999600-96001000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:95999600-96001200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr5:95999600-96001400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr5:95999600-96001400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr5:95999600-96001400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:95999600-96001800	Weak transcription	Small Intestine	intestine
16	chr5:95999600-96001800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr5:95999600-96002000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:95999600-96002000	Weak transcription	Colonic Mucosa	Colon
19	chr5:95999600-96002000	Weak transcription	Psoas Muscle	Psoas
20	chr5:95999600-96002200	Weak transcription	Esophagus	oesophagus
21	chr5:95999600-96003800	Weak transcription	Fetal Kidney	kidney
22	chr5:95999600-96003800	Weak transcription	Gastric	stomach
23	chr5:95999600-96004400	Weak transcription	Right Atrium	heart
24	chr5:95999600-96004600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:95999600-96004600	Weak transcription	Lung	lung
26	chr5:95999600-96004600	Weak transcription	Ovary	ovary
27	chr5:95999600-96006800	Weak transcription	Right Ventricle	heart
28	chr5:95999600-96006800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:95999600-96006800	Weak transcription	Spleen	Spleen
30	chr5:95999600-96012400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:95999600-96016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:95999600-96016600	Weak transcription	HSMMtube	muscle
33	chr5:95999600-96026000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:95999600-96028200	Weak transcription	Aorta	Aorta
35	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung
37	chr5:95999800-96001000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr5:95999800-96001000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr5:95999800-96001000	Enhancers	Adipose Nuclei	Adipose
40	chr5:95999800-96001000	Enhancers	Fetal Intestine Large	intestine
41	chr5:95999800-96001000	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr5:95999800-96001200	Enhancers	Fetal Intestine Small	intestine
43	chr5:95999800-96001800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:95999800-96004400	Weak transcription	GM12878-XiMat	blood
45	chr5:95999800-96010800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr5:95999800-96022800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:95999800-96024600	Weak transcription	Fetal Heart	heart
48	chr5:96000000-96001400	Enhancers	NHDF-Ad	bronchial
49	chr5:96000000-96005000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:96000400-96001200	Weak transcription	Primary monocytes fromperipheralblood	blood

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