Variant report

Variant	rs4902857
Chromosome Location	chr14:71267345-71267346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71251307..71253279-chr14:71267106..71269549,2	MCF-7	breast:
2	chr14:71265603..71269219-chr14:71272232..71276913,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10083428	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11847356	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11847373	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12590049	0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1548584	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108554	0.87[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs17176985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177097	0.81[ASW][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17766512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17766551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17766661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859460	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742847	0.91[EUR][1000 genomes]
rs4595741	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4899374	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4902858	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902859	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57284652	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57843652	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59858521	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60533515	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61988426	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61988427	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990472	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990476	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990481	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990518	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61990519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990520	0.88[EUR][1000 genomes]
rs61990521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990523	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990526	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61990527	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61990550	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990551	0.81[EUR][1000 genomes]
rs6573982	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6573983	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7141204	0.81[EUR][1000 genomes]
rs7150427	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7151024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757570	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8006715	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8018972	0.87[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs8019053	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs8020803	0.81[EUR][1000 genomes]
rs8021668	0.81[LWK][hapmap]
rs8022621	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4902857	HEATR4	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
2	chr14:71239000-71269600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:71247800-71274600	Weak transcription	Stomach Mucosa	stomach
4	chr14:71248200-71271200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr14:71249400-71274400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr14:71249400-71274400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr14:71249400-71274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr14:71249600-71274600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr14:71249800-71274600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr14:71252600-71268400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:71256600-71269600	Weak transcription	Brain Hippocampus Middle	brain
12	chr14:71257200-71274600	Weak transcription	Brain Anterior Caudate	brain
13	chr14:71257200-71274600	Weak transcription	Spleen	Spleen
14	chr14:71257800-71274800	Weak transcription	Colonic Mucosa	Colon
15	chr14:71259000-71274600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr14:71260000-71268600	Weak transcription	Esophagus	oesophagus
17	chr14:71260000-71274800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr14:71260200-71268200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr14:71261200-71270400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr14:71261200-71270600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr14:71261200-71271400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr14:71261200-71274600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr14:71261600-71272000	Weak transcription	Fetal Stomach	stomach
24	chr14:71262800-71268000	Strong transcription	A549	lung
25	chr14:71262800-71268600	Strong transcription	HMEC	breast
26	chr14:71263000-71267800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr14:71263400-71268600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:71264600-71267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr14:71264600-71268000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr14:71264600-71268800	Weak transcription	Brain Substantia Nigra	brain
31	chr14:71265000-71274600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr14:71265200-71274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr14:71265400-71268600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr14:71265600-71267800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr14:71265600-71269000	Strong transcription	HepG2	liver
36	chr14:71265800-71267800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr14:71265800-71268000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:71265800-71268400	Strong transcription	NHEK	skin
39	chr14:71265800-71274600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr14:71266200-71267800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:71266200-71267800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr14:71266200-71267800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr14:71266400-71267400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr14:71266400-71267600	Strong transcription	Primary B cells from cord blood	blood
45	chr14:71266400-71267600	Strong transcription	Fetal Intestine Large	intestine
46	chr14:71266400-71267600	Strong transcription	Placenta	Placenta
47	chr14:71266400-71267600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr14:71266400-71267800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr14:71266400-71267800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr14:71266400-71267800	Strong transcription	Primary B cells from peripheral blood	blood

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