Variant report

Variant	rs6990449
Chromosome Location	chr8:86130623-86130624
allele	A/G
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	chr8:86129821-86130780	GM12878	blood:	n/a	n/a
2	POLR2A	chr8:86130381-86131603	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr8:86129819-86133333	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:86129179..86130942-chr8:86131106..86134281,3	MCF-7	breast:
2	chr8:86088150..86092119-chr8:86130217..86134794,5	K562	blood:
3	chr8:86130126..86132730-chr8:86156867..86158422,2	K562	blood:
4	chr8:86088315..86091850-chr8:86128947..86134706,9	MCF-7	breast:

Variant related genes	Relation type
C8orf59	TF binding region
CA13	TF binding region
ENSG00000258256	Chromatin interaction
ENSG00000185015	Chromatin interaction
ENSG00000254208	Chromatin interaction
ENSG00000260493	Chromatin interaction
ENSG00000176731	Chromatin interaction
ENSG00000133740	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10088120	0.86[JPT][hapmap]
rs10090196	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10106970	0.82[ASN][1000 genomes]
rs1014303	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1021583	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11261468	0.93[JPT][hapmap]
rs11261471	0.86[JPT][hapmap]
rs11261472	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11261474	0.87[JPT][hapmap]
rs11989660	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12114575	0.81[ASN][1000 genomes]
rs12541445	0.86[JPT][hapmap]
rs12543256	0.93[JPT][hapmap]
rs12544332	0.81[JPT][hapmap]
rs12546106	0.93[JPT][hapmap]
rs12550160	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1303806	0.83[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs1303807	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13252971	0.87[JPT][hapmap]
rs13259399	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13269739	0.86[JPT][hapmap]
rs1390711	0.83[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1496529	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs1496530	0.87[JPT][hapmap]
rs1532423	0.81[JPT][hapmap]
rs1532424	0.87[JPT][hapmap]
rs1553015	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16913681	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs16913721	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17740658	0.93[JPT][hapmap]
rs1908762	0.86[JPT][hapmap]
rs1995056	0.84[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1995057	0.86[JPT][hapmap]
rs1995058	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2006767	1.00[JPT][hapmap]
rs2132589	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2278459	0.84[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2279701	0.87[JPT][hapmap]
rs2291786	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2291787	0.86[JPT][hapmap]
rs2403082	0.84[AMR][1000 genomes]
rs2403083	0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs2403085	0.87[JPT][hapmap]
rs2403086	0.87[JPT][hapmap]
rs2403088	0.93[JPT][hapmap]
rs2403089	0.85[AMR][1000 genomes]
rs2403104	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2548281	0.81[JPT][hapmap]
rs2645049	0.81[JPT][hapmap]
rs28564613	0.80[ASN][1000 genomes]
rs28677919	0.94[ASN][1000 genomes]
rs2896452	0.93[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2896453	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2896454	0.86[JPT][hapmap]
rs34103685	0.86[JPT][hapmap]
rs35285802	0.82[ASN][1000 genomes]
rs3779899	0.85[JPT][hapmap]
rs3779901	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3808538	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808539	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs4150867	0.87[JPT][hapmap]
rs4150868	0.87[JPT][hapmap]
rs4150869	0.80[JPT][hapmap]
rs4150893	0.86[JPT][hapmap]
rs4150909	0.86[JPT][hapmap]
rs4150942	0.84[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4150944	0.87[JPT][hapmap]
rs4150962	0.80[ASN][1000 genomes]
rs4150964	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4150974	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4150977	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4609189	0.93[JPT][hapmap]
rs4739700	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4739702	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4740043	0.87[JPT][hapmap]
rs4740044	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4740045	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4740048	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4740049	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62527225	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6605610	0.93[JPT][hapmap]
rs6605611	0.93[JPT][hapmap]
rs6605624	0.93[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs6605625	0.84[AMR][1000 genomes]
rs67573812	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987641	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6990452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6993387	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6994113	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs6997458	0.81[JPT][hapmap]
rs7001359	0.87[JPT][hapmap]
rs7004871	0.86[ASN][1000 genomes]
rs7007304	0.82[AMR][1000 genomes]
rs7008772	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7011001	0.80[ASN][1000 genomes]
rs7011926	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7015758	0.87[JPT][hapmap]
rs7818163	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7821629	0.81[ASN][1000 genomes]
rs7826589	0.93[JPT][hapmap]
rs7827175	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs7829050	0.87[JPT][hapmap]
rs7829144	0.93[JPT][hapmap]
rs7829240	0.82[ASN][1000 genomes]
rs7833737	0.82[EUR][1000 genomes]
rs7835303	0.81[ASN][1000 genomes]
rs7835882	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7837275	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7838900	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7841142	0.93[JPT][hapmap]
rs903895	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs903896	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs903897	0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6990449	LRRCC1	cis	Esophagus Mucosa	GTEx
rs6990449	C8orf59	cis	thalamus	BrainEAC
rs6990449	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs6990449	C8orf59	cis	inferior olivary nucleus	BrainEAC
rs6990449	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs6990449	C8orf59	cis	brain	BrainEAC
rs6990449	C8orf59	cis	temporal cortex	BrainEAC
rs6990449	C8orf59	cis	frontal cortex	BrainEAC
rs6990449	LRRCC1	cis	lesional skin	skin_eQTL
rs6990449	C8orf59	cis	occipital cortex	BrainEAC
rs6990449	C8orf59	cis	intralobular white matter	BrainEAC
rs6990449	C8orf59	cis	hippocampus	BrainEAC
rs6990449	C8orf59	cis	cerebellar cortex	BrainEAC

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	chr8:86119200-86131400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr8:86119400-86130800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr8:86119400-86131200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:86120200-86130800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr8:86120600-86131200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:86120800-86131200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr8:86120800-86131200	Strong transcription	Fetal Thymus	thymus
14	chr8:86121000-86131000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr8:86121400-86131000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:86121600-86132200	Weak transcription	Gastric	stomach
17	chr8:86122000-86131800	Weak transcription	Right Atrium	heart
18	chr8:86123200-86130800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr8:86124600-86130800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr8:86124600-86130800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr8:86124600-86131200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr8:86124800-86130800	Strong transcription	Placenta	Placenta
23	chr8:86125800-86131200	Weak transcription	Fetal Intestine Small	intestine
24	chr8:86126200-86130800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr8:86126800-86131600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr8:86126800-86131600	Weak transcription	NHLF	lung
27	chr8:86127200-86132000	Weak transcription	Stomach Mucosa	stomach
28	chr8:86127400-86132000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr8:86127600-86131200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr8:86127600-86131200	Strong transcription	Fetal Lung	lung
31	chr8:86127800-86131400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr8:86128000-86131800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr8:86128200-86131000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr8:86128600-86131200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr8:86128600-86131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr8:86128600-86131600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr8:86128600-86131800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr8:86128600-86131800	Weak transcription	Lung	lung
39	chr8:86128600-86131800	Weak transcription	Ovary	ovary
40	chr8:86128600-86131800	Weak transcription	Psoas Muscle	Psoas
41	chr8:86128600-86132000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr8:86128600-86132000	Weak transcription	HSMMtube	muscle
43	chr8:86128600-86132200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr8:86128600-86132200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr8:86128800-86130800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr8:86128800-86130800	Weak transcription	Pancreas	Pancrea
47	chr8:86128800-86131200	Weak transcription	Primary T cells from cord blood	blood
48	chr8:86128800-86131200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr8:86128800-86131200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr8:86128800-86131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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