Variant report

Variant	rs28377260
Chromosome Location	chr8:86128284-86128285
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:86128261-86128643	HCT-116	colon:	n/a	n/a
2	POLR2A	chr8:86128046-86128652	K562	blood:	n/a	n/a
3	POLR2A	chr8:86127491-86128897	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr8:86125551-86129403	K562	blood:	n/a	n/a
5	POLR2A	chr8:86127779-86128459	GM12891	blood:	n/a	n/a
6	POLR2A	chr8:86128210-86128929	HepG2	liver:	n/a	n/a
7	POLR2A	chr8:86128256-86128341	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr8:86127560-86129035	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr8:86127520-86128290	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr8:86128076-86128495	K562	blood:	n/a	n/a
11	POLR2A	chr8:86127416-86128566	HepG2	liver:	n/a	n/a
12	POLR2A	chr8:86127500-86128969	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86119264..86121436-chr8:86127693..86129609,2	MCF-7	breast:

Variant related genes	Relation type
CA13	TF binding region
C8orf59	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10090196	0.81[EUR][1000 genomes]
rs10091577	0.81[EUR][1000 genomes]
rs10091710	0.82[EUR][1000 genomes]
rs10106970	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021583	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11261469	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11261471	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12541299	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12541445	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12543256	0.88[ASN][1000 genomes]
rs12546106	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12550160	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12679400	0.85[ASN][1000 genomes]
rs13259464	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13269031	0.81[EUR][1000 genomes]
rs16913681	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16913721	0.82[EUR][1000 genomes]
rs17740658	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1845891	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1845892	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1908762	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2006767	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2132589	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2132590	0.86[ASN][1000 genomes]
rs2279700	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2279701	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291786	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2403083	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2403084	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2403085	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2403086	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28439950	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28564613	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28677919	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3779901	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150865	0.81[EUR][1000 genomes]
rs4150867	0.82[EUR][1000 genomes]
rs4150868	0.82[EUR][1000 genomes]
rs4150869	0.82[EUR][1000 genomes]
rs4150884	0.83[EUR][1000 genomes]
rs4150893	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4150897	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4150909	0.82[ASN][1000 genomes]
rs4150942	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4150944	0.84[ASN][1000 genomes]
rs4150962	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150964	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150977	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4609189	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4617148	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4739698	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4740045	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4740047	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62527173	0.82[EUR][1000 genomes]
rs6605610	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6605611	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6993316	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6994113	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7001359	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7004871	0.82[EUR][1000 genomes]
rs7011001	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7821629	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7827175	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7829240	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7839129	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7842013	0.82[EUR][1000 genomes]
rs9329908	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28377260	LRRCC1	cis	Artery Tibial	GTEx
rs28377260	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs28377260	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs28377260	LRRCC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86091000-86132000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:86101200-86131000	Weak transcription	HepG2	liver
3	chr8:86113200-86131200	Weak transcription	Fetal Heart	heart
4	chr8:86113400-86132000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr8:86114200-86131200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:86114400-86131200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:86114800-86130600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr8:86119200-86131400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:86119400-86130800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr8:86119400-86131200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr8:86120200-86130800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr8:86120600-86131200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:86120800-86128800	Strong transcription	Brain Germinal Matrix	brain
14	chr8:86120800-86129000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr8:86120800-86131200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr8:86120800-86131200	Strong transcription	Fetal Thymus	thymus
17	chr8:86121000-86129000	Strong transcription	Fetal Muscle Leg	muscle
18	chr8:86121000-86129400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr8:86121000-86129600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr8:86121000-86130200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr8:86121000-86130400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr8:86121000-86131000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr8:86121400-86128600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr8:86121400-86129000	Strong transcription	Fetal Intestine Large	intestine
25	chr8:86121400-86129800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr8:86121400-86131000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr8:86121600-86132200	Weak transcription	Gastric	stomach
28	chr8:86122000-86131800	Weak transcription	Right Atrium	heart
29	chr8:86123200-86130800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr8:86123800-86129000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr8:86124000-86129400	Strong transcription	Liver	Liver
32	chr8:86124000-86129400	Strong transcription	GM12878-XiMat	blood
33	chr8:86124000-86129800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr8:86124000-86129800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr8:86124000-86130200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr8:86124000-86130200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr8:86124000-86130400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr8:86124000-86130600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr8:86124200-86128800	Strong transcription	Primary T cells from cord blood	blood
40	chr8:86124200-86129000	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr8:86124200-86129400	Strong transcription	NH-A	brain
42	chr8:86124200-86129600	Strong transcription	HMEC	breast
43	chr8:86124200-86130600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr8:86124200-86130600	Strong transcription	Dnd41	blood
45	chr8:86124400-86129200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr8:86124400-86129400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr8:86124400-86129600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr8:86124400-86129800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr8:86124400-86130600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr8:86124600-86128800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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