Variant report

Variant	rs28629346
Chromosome Location	chr7:100044551-100044552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100024880..100026635-chr7:100043606..100045872,2	MCF-7	breast:
2	chr7:100042705..100044790-chr7:100067087..100068632,2	K562	blood:
3	chr7:100042770..100045567-chr7:100486331..100489314,2	MCF-7	breast:
4	chr7:100042589..100045282-chr7:100051285..100054140,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176125	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 44 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1000215	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1073	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11559117	1.00[ASN][1000 genomes]
rs11761624	1.00[ASN][1000 genomes]
rs11761725	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761784	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763414	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11763511	1.00[ASN][1000 genomes]
rs11764818	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766202	1.00[ASN][1000 genomes]
rs11766752	1.00[ASN][1000 genomes]
rs11769700	1.00[ASN][1000 genomes]
rs11769886	0.93[EUR][1000 genomes]
rs11771241	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11771419	0.81[EUR][1000 genomes]
rs11772580	1.00[ASN][1000 genomes]
rs11773661	1.00[ASN][1000 genomes]
rs1962269	1.00[ASN][1000 genomes]
rs2003507	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2406253	1.00[ASN][1000 genomes]
rs2406255	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28490152	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28578163	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28660238	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2897358	1.00[ASN][1000 genomes]
rs34989573	1.00[ASN][1000 genomes]
rs35111986	0.93[EUR][1000 genomes]
rs3900792	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4074838	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4385401	1.00[ASN][1000 genomes]
rs4463351	1.00[ASN][1000 genomes]
rs4469386	1.00[ASN][1000 genomes]
rs4472444	1.00[ASN][1000 genomes]
rs4989959	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60257855	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60478351	1.00[ASN][1000 genomes]
rs60644673	1.00[ASN][1000 genomes]
rs60844404	1.00[ASN][1000 genomes]
rs66632384	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66648318	1.00[ASN][1000 genomes]
rs66958101	1.00[ASN][1000 genomes]
rs67040465	0.86[ASN][1000 genomes]
rs67163493	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67196635	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67239991	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67315960	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67471932	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67483801	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67885733	1.00[ASN][1000 genomes]
rs68116612	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6948699	1.00[ASN][1000 genomes]
rs6953107	1.00[ASN][1000 genomes]
rs6953749	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6955362	1.00[ASN][1000 genomes]
rs6957928	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6962151	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970806	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6970828	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6972167	0.86[ASN][1000 genomes]
rs6974286	1.00[ASN][1000 genomes]
rs6975514	1.00[ASN][1000 genomes]
rs6975729	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978739	1.00[ASN][1000 genomes]
rs6979335	1.00[ASN][1000 genomes]
rs73161759	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73161762	0.95[EUR][1000 genomes]
rs73403312	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73405353	1.00[ASN][1000 genomes]
rs7783159	0.96[EUR][1000 genomes]
rs7783550	0.81[EUR][1000 genomes]
rs7787620	1.00[ASN][1000 genomes]
rs7787825	1.00[ASN][1000 genomes]
rs7794485	1.00[ASN][1000 genomes]
rs7800667	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803454	0.91[EUR][1000 genomes]
rs7809801	1.00[ASN][1000 genomes]
rs7811142	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv831071	chr7:99918025-100113413	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers 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	287 gene(s)	inside rSNPs	diseases
4	nsv527107	chr7:100014711-100064719	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	269 gene(s)	inside rSNPs	diseases
5	nsv888776	chr7:100014711-100198386	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
6	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
7	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
8	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
9	nsv888780	chr7:100032665-100198386	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS 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	81 gene(s)	inside rSNPs	diseases
10	nsv984550	chr7:100034415-100080060	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:44)

SNP	Gene	Cis/trans	Tissue	Source
rs28629346	PILRB	cis	Artery Aorta	GTEx
rs28629346	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs28629346	PILRA	cis	Thyroid	GTEx
rs28629346	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs28629346	STAG3L5P	cis	Muscle Skeletal	GTEx
rs28629346	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs28629346	STAG3L5P	cis	Nerve Tibial	GTEx
rs28629346	ZCWPW1	cis	Nerve Tibial	GTEx
rs28629346	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs28629346	STAG3L5P	cis	Artery Tibial	GTEx
rs28629346	PILRB	cis	Artery Tibial	GTEx
rs28629346	PILRB	cis	Thyroid	GTEx
rs28629346	STAG3L5P	cis	Artery Aorta	GTEx
rs28629346	PILRB	cis	Esophagus Muscularis	GTEx
rs28629346	PILRB	cis	lung	GTEx
rs28629346	STAG3L5P	cis	Stomach	GTEx
rs28629346	PVRIG2P	cis	lung	GTEx
rs28629346	PVRIG2P	cis	Artery Tibial	GTEx
rs28629346	PILRA	cis	Adipose Subcutaneous	GTEx
rs28629346	PVRIG2P	cis	Thyroid	GTEx
rs28629346	PILRB	cis	Heart Left Ventricle	GTEx
rs28629346	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs28629346	PILRA	cis	Esophagus Mucosa	GTEx
rs28629346	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs28629346	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs28629346	PILRB	cis	Muscle Skeletal	GTEx
rs28629346	PILRA	cis	Artery Aorta	GTEx
rs28629346	PILRB	cis	Nerve Tibial	GTEx
rs28629346	PILRA	cis	Esophagus Muscularis	GTEx
rs28629346	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs28629346	STAG3L5P	cis	lung	GTEx
rs28629346	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs28629346	PILRA	cis	Artery Tibial	GTEx
rs28629346	PILRB	cis	Adipose Subcutaneous	GTEx
rs28629346	STAG3L5P	cis	Thyroid	GTEx
rs28629346	PILRB	cis	Esophagus Mucosa	GTEx
rs28629346	PILRB	cis	Whole Blood	GTEx
rs28629346	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs28629346	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs28629346	PILRA	cis	Muscle Skeletal	GTEx
rs28629346	PILRA	cis	Nerve Tibial	GTEx
rs28629346	PMS2P1	cis	Thyroid	GTEx
rs28629346	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs28629346	PILRA	cis	Heart Left Ventricle	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100034600-100047800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:100034600-100047800	Weak transcription	Brain Angular Gyrus	brain
3	chr7:100034600-100047800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:100034600-100047800	Weak transcription	Esophagus	oesophagus
5	chr7:100034600-100047800	Weak transcription	Fetal Brain Female	brain
6	chr7:100034600-100047800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:100035000-100047800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr7:100035200-100047800	Weak transcription	Thymus	Thymus
9	chr7:100037000-100047800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:100040000-100044600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr7:100042200-100047600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr7:100042400-100047600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:100042400-100047800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:100042600-100047800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:100042600-100047800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:100042600-100047800	Weak transcription	Psoas Muscle	Psoas
17	chr7:100042600-100048000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:100042800-100047200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:100042800-100047600	Weak transcription	Right Ventricle	heart
20	chr7:100042800-100047800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:100042800-100047800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:100042800-100047800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:100042800-100047800	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:100042800-100047800	Weak transcription	Colonic Mucosa	Colon
25	chr7:100042800-100047800	Weak transcription	Fetal Heart	heart
26	chr7:100042800-100047800	Weak transcription	Pancreas	Pancrea
27	chr7:100043000-100046600	Weak transcription	Liver	Liver
28	chr7:100043000-100047400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:100043000-100047600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr7:100043000-100047800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr7:100043000-100047800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr7:100043000-100047800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:100043000-100047800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:100043000-100047800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:100043000-100047800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr7:100043000-100047800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr7:100043000-100047800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr7:100043000-100047800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:100043200-100047000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr7:100043200-100047800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr7:100043200-100047800	Weak transcription	Right Atrium	heart
42	chr7:100043400-100047200	Weak transcription	Fetal Intestine Small	intestine
43	chr7:100043400-100047600	Weak transcription	Adipose Nuclei	Adipose
44	chr7:100043400-100047800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:100043400-100047800	Weak transcription	GM12878-XiMat	blood
46	chr7:100043800-100044600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:100044000-100047800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr7:100044200-100044600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr7:100044200-100044600	Enhancers	Lung	lung
50	chr7:100044200-100045600	Weak transcription	Primary monocytes fromperipheralblood	blood

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