Variant report

Variant	rs12550160
Chromosome Location	chr8:86134784-86134785
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86125325..86127241-chr8:86134278..86135853,2	K562	blood:
2	chr8:86088150..86092119-chr8:86130217..86134794,5	K562	blood:

Variant related genes	Relation type
ENSG00000260493	Chromatin interaction
ENSG00000254208	Chromatin interaction
ENSG00000133740	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10088120	0.95[JPT][hapmap]
rs10090196	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10091582	0.82[ASN][1000 genomes]
rs10099251	0.82[ASN][1000 genomes]
rs10100442	0.89[JPT][hapmap]
rs10106970	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110461	0.82[ASN][1000 genomes]
rs10111971	0.82[ASN][1000 genomes]
rs1021583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11261468	0.85[JPT][hapmap]
rs11261469	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11261471	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11261474	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12541299	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12541445	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12543256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12544332	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12546106	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12679400	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1303806	0.87[JPT][hapmap]
rs13252971	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs13259399	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs13259464	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13269739	0.95[JPT][hapmap]
rs1390711	0.87[JPT][hapmap]
rs1496529	0.83[JPT][hapmap]
rs1496530	0.82[JPT][hapmap]
rs1496531	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496532	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1532424	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1553015	0.86[JPT][hapmap]
rs1553016	0.82[ASN][1000 genomes]
rs1553017	0.82[ASN][1000 genomes]
rs16913681	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16913721	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17740658	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1845891	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1845892	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1908762	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1995056	0.81[JPT][hapmap]
rs1995057	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1995058	0.86[JPT][hapmap]
rs2006767	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132590	0.89[ASN][1000 genomes]
rs2278459	0.85[JPT][hapmap]
rs2279700	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279701	0.92[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291786	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291787	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2403083	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2403084	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2403085	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2403086	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2403088	0.85[JPT][hapmap]
rs2403104	0.86[JPT][hapmap]
rs28374336	0.82[ASN][1000 genomes]
rs28377260	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28439950	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28564613	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28677919	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2896452	0.85[JPT][hapmap]
rs2896454	0.95[JPT][hapmap]
rs34103685	0.95[JPT][hapmap]
rs35558766	0.82[ASN][1000 genomes]
rs3779899	0.95[JPT][hapmap]
rs3779901	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808538	0.82[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs3808539	0.86[JPT][hapmap]
rs4150867	0.95[JPT][hapmap]
rs4150868	0.95[JPT][hapmap]
rs4150869	0.90[JPT][hapmap]
rs4150893	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4150897	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4150909	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4150942	0.85[JPT][hapmap]
rs4150944	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4150962	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150964	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4609189	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4617148	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4739698	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4739700	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4740043	0.81[JPT][hapmap]
rs4740044	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4740045	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4740047	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4740049	0.86[JPT][hapmap]
rs6605610	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6605611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6605613	0.82[ASN][1000 genomes]
rs6605624	0.85[JPT][hapmap]
rs67573812	0.82[ASN][1000 genomes]
rs6987641	0.80[ASN][1000 genomes]
rs6990449	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs6990452	0.82[ASN][1000 genomes]
rs6993316	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6993387	0.91[JPT][hapmap]
rs6994113	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7001359	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7004871	0.86[EUR][1000 genomes]
rs7008772	0.91[JPT][hapmap]
rs7011001	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7011926	0.86[JPT][hapmap]
rs7015758	0.95[JPT][hapmap]
rs7818163	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7821629	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7826589	0.81[JPT][hapmap]
rs7827175	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7829050	0.95[JPT][hapmap]
rs7829144	0.85[JPT][hapmap]
rs7829240	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7839129	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7841142	0.85[JPT][hapmap]
rs903895	0.86[JPT][hapmap]
rs903896	0.86[JPT][hapmap]
rs903897	0.87[JPT][hapmap]
rs9329908	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
3	nsv971329	chr8:86094967-86183119	Weak transcription Strong transcription Enhancers 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 miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12550160	LRRCC1	cis	Artery Tibial	GTEx
rs12550160	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs12550160	CA13	cis	multi-tissue	Pritchard
rs12550160	CA13	cis	Lymphoblastoid	GTEx
rs12550160	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs12550160	LRRCC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86131400-86135000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:86131600-86135000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr8:86131600-86135400	Active TSS	GM12878-XiMat	blood
4	chr8:86131800-86134800	Active TSS	Fetal Intestine Small	intestine
5	chr8:86132000-86134800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr8:86132000-86135200	Active TSS	Fetal Intestine Large	intestine
7	chr8:86133000-86143200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:86133000-86145800	Weak transcription	Gastric	stomach
9	chr8:86133200-86135000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr8:86133200-86135200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr8:86133600-86135200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr8:86133600-86135600	Weak transcription	Osteobl	bone
13	chr8:86133600-86137200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr8:86133800-86135200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:86133800-86135200	Active TSS	Duodenum Mucosa	Duodenum
16	chr8:86133800-86157200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr8:86134000-86135000	Enhancers	Primary B cells from peripheral blood	blood
18	chr8:86134000-86135000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr8:86134000-86135000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr8:86134000-86135800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr8:86134200-86134800	Active TSS	Primary T cells from cord blood	blood
22	chr8:86134200-86134800	Enhancers	Primary hematopoietic stem cells	blood
23	chr8:86134200-86134800	Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr8:86134200-86134800	Weak transcription	Esophagus	oesophagus
25	chr8:86134200-86134800	Weak transcription	Fetal Lung	lung
26	chr8:86134200-86135000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr8:86134200-86135000	Enhancers	K562	blood
28	chr8:86134200-86135200	Enhancers	Primary B cells from cord blood	blood
29	chr8:86134200-86135600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr8:86134200-86136000	Enhancers	Liver	Liver
31	chr8:86134200-86136200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr8:86134200-86136400	Enhancers	NHEK	skin
33	chr8:86134400-86134800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:86134400-86134800	Enhancers	Rectal Smooth Muscle	rectum
35	chr8:86134400-86135000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr8:86134400-86135000	Weak transcription	Stomach Mucosa	stomach
37	chr8:86134400-86135000	Enhancers	Dnd41	blood
38	chr8:86134400-86135800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr8:86134400-86137000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr8:86134600-86134800	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr8:86134600-86134800	Flanking Active TSS	Fetal Kidney	kidney
42	chr8:86134600-86135000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr8:86134600-86135000	Enhancers	Thymus	Thymus
44	chr8:86134600-86135000	Flanking Active TSS	HMEC	breast
45	chr8:86134600-86135200	Flanking Active TSS	HepG2	liver
46	chr8:86134600-86136200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr8:86134600-86157200	Weak transcription	Right Atrium	heart

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