Variant report

Variant	rs4877797
Chromosome Location	chr9:86306213-86306214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86304049..86306359-chr9:86307807..86310071,2	K562	blood:
2	chr9:86300921..86303072-chr9:86304972..86308780,3	MCF-7	breast:
3	chr9:86300623..86303382-chr9:86303567..86306899,3	K562	blood:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10512136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10512137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1056073	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10746717	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10780616	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10780617	0.87[AMR][1000 genomes]
rs10780618	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes]
rs10780619	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10780620	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10780622	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10780623	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10780624	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10780625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10868036	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10868037	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10868038	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868042	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10868043	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11140198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11140202	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140209	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11140212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11140221	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11140223	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11791175	1.00[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12235741	0.82[AMR][1000 genomes]
rs1333861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1333862	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1537502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1537503	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs17080575	0.82[AMR][1000 genomes]
rs1961941	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2282220	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2811921	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs3750409	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3750410	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs3814505	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3814507	0.82[AMR][1000 genomes]
rs4146740	0.82[EUR][1000 genomes]
rs4454364	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877790	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4877791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4877793	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877796	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4877799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877800	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7046388	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72618136	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7860614	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7863266	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7866234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7871055	0.90[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs868917	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4877797	RP11-522I20.3	cis	Muscle Skeletal	GTEx
rs4877797	RP11-522I20.3	cis	Whole Blood	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86280400-86307400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:86289000-86308200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
4	chr9:86291400-86314400	Weak transcription	Fetal Heart	heart
5	chr9:86292800-86308600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:86293600-86317000	Weak transcription	NHLF	lung
7	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:86294200-86314200	Weak transcription	Gastric	stomach
9	chr9:86294200-86315600	Weak transcription	Right Ventricle	heart
10	chr9:86294200-86320000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:86295000-86308800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:86295000-86313600	Weak transcription	Lung	lung
13	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
14	chr9:86296200-86316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:86296800-86306400	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:86296800-86314200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:86297000-86315600	Weak transcription	HMEC	breast
18	chr9:86297000-86315600	Weak transcription	HSMM	muscle
19	chr9:86297000-86320000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr9:86297600-86310800	Weak transcription	Fetal Lung	lung
21	chr9:86297600-86314400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:86297600-86319800	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:86297600-86321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:86297800-86311600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:86297800-86314800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:86297800-86315800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:86298000-86307800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr9:86298000-86308000	Weak transcription	Primary B cells from cord blood	blood
29	chr9:86298000-86308200	Weak transcription	K562	blood
30	chr9:86298000-86313600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:86298000-86314200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:86298000-86315400	Weak transcription	HepG2	liver
33	chr9:86298000-86315600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:86298000-86316600	Weak transcription	Thymus	Thymus
35	chr9:86298000-86316800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:86298000-86320400	Weak transcription	Fetal Intestine Large	intestine
37	chr9:86298200-86311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:86298200-86317000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:86298200-86317600	Weak transcription	Dnd41	blood
40	chr9:86298600-86320400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr9:86298800-86320800	Weak transcription	Fetal Thymus	thymus
42	chr9:86299600-86313600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:86299600-86319400	Weak transcription	Fetal Stomach	stomach
44	chr9:86299600-86320000	Weak transcription	Fetal Intestine Small	intestine
45	chr9:86300000-86310800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr9:86300000-86313800	Weak transcription	HUVEC	blood vessel
47	chr9:86300200-86306400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr9:86300200-86313000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:86300200-86313000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:86300200-86313000	Weak transcription	A549	lung

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