Variant report

Variant	rs4971100
Chromosome Location	chr1:155155731-155155732
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	chr1:155030728..155033754-chr1:155154705..155158020,3	K562	blood:
2	chr1:155099738..155102242-chr1:155155678..155157548,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143537	Chromatin interaction
ENSG00000169242	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1057941	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264337	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11264338	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs11264339	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs11264341	0.96[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12028043	0.82[CHD][hapmap]
rs12411216	0.81[ASN][1000 genomes]
rs2066981	0.81[JPT][hapmap]
rs2070803	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075570	0.80[ASN][1000 genomes]
rs2075571	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28445596	0.80[ASN][1000 genomes]
rs2974935	0.81[ASN][1000 genomes]
rs2974937	0.81[ASN][1000 genomes]
rs3814316	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4072037	0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs423144	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4421576	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs4460629	0.82[CHD][hapmap]
rs4971059	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4971066	0.93[CHB][hapmap];0.87[CHD][hapmap]
rs4971073	0.93[CHB][hapmap];0.94[CHD][hapmap]
rs4971079	0.81[CHD][hapmap]
rs4971085	0.82[JPT][hapmap]
rs4971088	0.91[JPT][hapmap]
rs4971093	0.90[ASN][1000 genomes]
rs4971099	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971101	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7366775	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7556304	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs914615	0.91[JPT][hapmap]
rs9426886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
4	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
6	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
7	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
9	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
11	nsv8447	chr1:155144629-155156937	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
12	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
13	nsv872458	chr1:155146102-155180466	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	316 gene(s)	inside rSNPs	diseases
14	nsv872459	chr1:155149718-155169633	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	308 gene(s)	inside rSNPs	diseases
15	nsv527682	chr1:155149718-155197462	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	361 gene(s)	inside rSNPs	diseases
16	nsv872460	chr1:155151493-155163181	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv872461	chr1:155151493-155169633	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	308 gene(s)	inside rSNPs	diseases
18	nsv872462	chr1:155151493-155172177	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	308 gene(s)	inside rSNPs	diseases
19	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
20	nsv872463	chr1:155155731-155169633	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	308 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4971100	SLC39A1	cis	multi-tissue	Pritchard
rs4971100	UBE2Q1	cis	cerebellum	SCAN
rs4971100	GBAP1	cis	Artery Tibial	GTEx
rs4971100	GBAP1	cis	lung	GTEx
rs4971100	MUC1	cis	Esophagus Mucosa	GTEx
rs4971100	SLC39A1	cis	parietal	SCAN
rs4971100	GBAP1	cis	Artery Aorta	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155146400-155157600	Weak transcription	Right Atrium	heart
2	chr1:155146600-155163000	Weak transcription	Aorta	Aorta
3	chr1:155147600-155157200	Weak transcription	Right Ventricle	heart
4	chr1:155148400-155157800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:155149400-155157400	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr1:155149600-155156600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:155149600-155156800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr1:155149600-155157400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:155149600-155157400	Weak transcription	Fetal Intestine Large	intestine
10	chr1:155149600-155158000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:155149600-155158200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:155149600-155158800	Weak transcription	A549	lung
13	chr1:155149600-155162000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:155149600-155162600	Weak transcription	Small Intestine	intestine
15	chr1:155149600-155162800	Weak transcription	NHDF-Ad	bronchial
16	chr1:155149800-155155800	Weak transcription	Spleen	Spleen
17	chr1:155149800-155156600	Strong transcription	Brain Cingulate Gyrus	brain
18	chr1:155149800-155156800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:155149800-155157000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:155149800-155157600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:155149800-155157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:155149800-155158400	Strong transcription	Brain Germinal Matrix	brain
23	chr1:155149800-155158800	Strong transcription	Fetal Stomach	stomach
24	chr1:155149800-155162000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:155149800-155162200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:155150000-155158400	Weak transcription	NHEK	skin
27	chr1:155150000-155162000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:155150000-155163000	Weak transcription	Fetal Brain Male	brain
29	chr1:155150200-155162400	Weak transcription	Dnd41	blood
30	chr1:155150400-155156800	Weak transcription	GM12878-XiMat	blood
31	chr1:155150400-155157400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:155150400-155161800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:155150600-155162000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:155150800-155161800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:155151000-155156200	Weak transcription	Esophagus	oesophagus
36	chr1:155151000-155162000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:155151200-155162000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:155151800-155156200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:155152000-155157200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr1:155152200-155157200	Weak transcription	Colonic Mucosa	Colon
41	chr1:155152200-155157800	Strong transcription	Fetal Brain Female	brain
42	chr1:155152200-155162800	Weak transcription	Osteobl	bone
43	chr1:155152400-155163000	Weak transcription	HUVEC	blood vessel
44	chr1:155152600-155155800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:155152600-155156200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:155152600-155157600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:155152600-155161800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:155152600-155161800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:155152600-155162000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:155152600-155162200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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