Variant report

Variant	rs9380618
Chromosome Location	chr6:36853543-36853544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:609)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:609 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:36853362-36854002	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr6:36853319-36853749	H1-hESC	embryonic stem cell:	n/a	chr6:36853552-36853568
3	CTCF	chr6:36853480-36853630	HepG2	liver:	n/a	chr6:36853552-36853568
4	TCF12	chr6:36853453-36853652	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr6:36853444-36854039	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3AK20	chr6:36853340-36854225	SK-N-SH	brain:	n/a	n/a
7	BCL3	chr6:36853357-36853933	A549	lung:	n/a	n/a
8	NFIC	chr6:36853327-36854266	GM12878	blood:	n/a	n/a
9	CHD2	chr6:36853186-36853962	Hela-S3	cervix:	n/a	chr6:36853588-36853597
10	CTCF	chr6:36853480-36853630	HUVEC	blood vessel:	n/a	chr6:36853552-36853568
11	CTCF	chr6:36853500-36853650	RPTEC	kidney:	n/a	chr6:36853552-36853568
12	POLR2A	chr6:36853458-36854119	MCF-7	breast:	n/a	n/a
13	REST	chr6:36853054-36854391	H1-neurons	neurons:	n/a	chr6:36853978-36853988 chr6:36853977-36853990
14	CTCF	chr6:36853319-36853682	SK-N-SH_RA	brain:	n/a	chr6:36853552-36853568
15	ZKSCAN1	chr6:36853282-36853848	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr6:36853520-36853670	WI-38	lung:	n/a	chr6:36853552-36853568
17	NR2C2	chr6:36853385-36854088	HepG2	liver:	n/a	n/a
18	CEBPB	chr6:36853248-36853853	K562	blood:	n/a	n/a
19	ARID3A	chr6:36853225-36853830	HepG2	liver:	n/a	n/a
20	MAX	chr6:36853437-36854146	K562	blood:	n/a	n/a
21	EGR1	chr6:36853393-36854092	K562	blood:	n/a	n/a
22	POU2F2	chr6:36853242-36853978	GM12878	blood:	n/a	n/a
23	CTCF	chr6:36853372-36853729	Gliobla	brain:	n/a	chr6:36853552-36853568
24	TAF1	chr6:36853252-36853906	PFSK-1	brain:	n/a	n/a
25	SIN3AK20	chr6:36853371-36853969	PFSK-1	brain:	n/a	n/a
26	SIN3AK20	chr6:36853432-36853811	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:36853472-36854064	MCF-7	breast:	n/a	n/a
28	YY1	chr6:36853369-36853822	SK-N-SH_RA	brain:	n/a	n/a
29	POLR2A	chr6:36853365-36854209	HEK293	kidney:	n/a	n/a
30	MYC	chr6:36853313-36854149	NB4	blood:	n/a	n/a
31	POLR2A	chr6:36853253-36853994	HCT-116	colon:	n/a	n/a
32	POU2F2	chr6:36853431-36853763	GM12891	blood:	n/a	n/a
33	POLR2A	chr6:36853245-36853993	HepG2	liver:	n/a	n/a
34	TAF1	chr6:36853438-36853848	GM12891	blood:	n/a	n/a
35	CTCF	chr6:36853500-36853650	HMF	breast:	n/a	chr6:36853552-36853568
36	ZNF143	chr6:36853381-36853929	Hela-S3	cervix:	n/a	n/a
37	TAF1	chr6:36853470-36853933	HepG2	liver:	n/a	n/a
38	CTCF	chr6:36853480-36853630	BJ	skin:	n/a	chr6:36853552-36853568
39	CTCF	chr6:36853480-36853630	HA-sp	spinal cord:	n/a	chr6:36853552-36853568
40	POLR2A	chr6:36853153-36854206	GM12892	blood:	n/a	n/a
41	TAF1	chr6:36853423-36853997	HepG2	liver:	n/a	n/a
42	HNF4A	chr6:36853370-36853931	HepG2	liver:	n/a	n/a
43	ATF2	chr6:36853255-36853922	GM12878	blood:	n/a	n/a
44	CTCF	chr6:36853420-36853570	HCM	heart:	n/a	chr6:36853552-36853568
45	STAT3	chr6:36853432-36853741	GM12878	blood:	n/a	n/a
46	YY1	chr6:36853349-36853822	GM12878	blood:	n/a	n/a
47	MAX	chr6:36853354-36854141	NB4	blood:	n/a	n/a
48	CTCF	chr6:36853440-36853590	HCM	heart:	n/a	chr6:36853552-36853568
49	MAZ	chr6:36853363-36854074	K562	blood:	n/a	n/a
50	BCLAF1	chr6:36853391-36854217	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:36853529-36853579	AG04449	skin:	fetal
2	chr6:36853529-36853579	NB4	blood:	n/a
3	chr6:36853529-36853579	HPAEpiC	pulmonary alveolar:	n/a
4	chr6:36853529-36853579	SK-N-MC	brain:	n/a
5	chr6:36853529-36853579	HL-60	blood:	n/a
6	chr6:36853529-36853579	HMEC	breast:	n/a
7	chr6:36853529-36853579	HEK293	kidney:	embryo
8	chr6:36853529-36853579	SK-N-SH	brain:	n/a
9	chr6:36853529-36853579	SAEC	small airway:	n/a
10	chr6:36853529-36853579	K562	blood:	n/a
11	chr6:36853529-36853579	AoSMC	blood vessel:	n/a
12	chr6:36853529-36853579	HIPEpiC	eye:	n/a
13	chr6:36853529-36853579	T-47D	breast:	n/a
14	chr6:36853529-36853579	HNPCEpiC	eye:	n/a
15	chr6:36853529-36853579	HRPEpiC	eye:	n/a
16	chr6:36853529-36853579	GM12892	blood:	n/a
17	chr6:36853529-36853579	AG04450	lung:	fetal
18	chr6:36853529-36853579	HEEpiC	esophagus:	n/a
19	chr6:36853529-36853579	BJ	skin:	n/a
20	chr6:36853529-36853579	LNCaP	prostate:	n/a
21	chr6:36853529-36853579	GM06990	blood:	n/a
22	chr6:36853529-36853579	IMR90	lung:	fetal
23	chr6:36853529-36853579	ovcar-3	ovarian:	n/a
24	chr6:36853529-36853579	NHDF-neo	bronchial:	n/a
25	chr6:36853529-36853579	HAEpiC	amniotic membrane:	n/a
26	chr6:36853529-36853579	MCF-7	breast:	n/a
27	chr6:36853529-36853579	AG09309	skin:	n/a
28	chr6:36853529-36853579	HCM	heart:	n/a
29	chr6:36853529-36853579	GM19239	blood:	n/a
30	chr6:36853529-36853579	Hela-S3	cervix:	n/a
31	chr6:36853529-36853579	ECC-1	luminal epithelium:	n/a
32	chr6:36853529-36853579	Caco-2	colon:	n/a
33	chr6:36853529-36853579	AG09319	gingival:	n/a
34	chr6:36853529-36853579	SKMC	muscle:	n/a
35	chr6:36853529-36853579	PANC-1	pancreas:	n/a
36	chr6:36853529-36853579	BE2_C	brain:	n/a
37	chr6:36853529-36853579	HUVEC	blood vessel:	n/a
38	chr6:36853529-36853579	HCT-116	colon:	n/a
39	chr6:36853529-36853579	U87	brain:	n/a
40	chr6:36853529-36853579	HCPEpiC	choroid plexus:	n/a
41	chr6:36853529-36853579	NHBE	bronchial:	n/a
42	chr6:36853529-36853579	HRE	kidney:	n/a
43	chr6:36853529-36853579	H1-hESC	embryonic stem cell:	embryo
44	chr6:36853529-36853579	HRCEpiC	kidney:	n/a
45	chr6:36853529-36853579	NH-A	brain:	n/a
46	chr6:36853529-36853579	RPTEC	kidney:	n/a
47	chr6:36853529-36853579	GM12878	blood:	n/a
48	chr6:36853529-36853579	PFSK-1	brain:	n/a
49	chr6:36853529-36853579	NT2-D1	testis:	n/a
50	chr6:36853529-36853579	A549	lung:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:22292249..22292768-chr6:36853269..36853777,2	K562	blood:
2	chr13:32888988..32889628-chr6:36853240..36854214,2	Hela-S3	cervix:
3	chr6:36841771..36843991-chr6:36852556..36855136,3	MCF-7	breast:
4	chr6:36852278..36855515-chr6:36952430..36957026,4	MCF-7	breast:
5	chr6:36803997..36809047-chr6:36852852..36856509,4	K562	blood:
6	chr16:18812518..18813383-chr6:36853356..36854075,2	Hela-S3	cervix:
7	chr6:36852138..36856054-chr6:36953606..36956862,5	K562	blood:
8	chr6:36841338..36845965-chr6:36851992..36855231,4	MCF-7	breast:
9	chr6:36560243..36562699-chr6:36853442..36856379,2	K562	blood:

No data

Variant related genes	Relation type
C6orf89	TF binding region
C6orf89	CpG island
ENSG00000224086	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000260342	Chromatin interaction
ENSG00000137168	Chromatin interaction
ENSG00000124772	Chromatin interaction
ENSG00000139618	Chromatin interaction
ENSG00000170540	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000189167	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1022696	0.85[YRI][hapmap]
rs10947647	0.85[YRI][hapmap]
rs1150784	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11759850	0.85[YRI][hapmap]
rs12528273	0.81[JPT][hapmap]
rs2116447	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272275	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs2272276	0.80[LWK][hapmap];0.85[YRI][hapmap]
rs2293393	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303993	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236349	0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs236352	0.96[ASN][1000 genomes]
rs236385	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs236386	0.80[CHB][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs2395663	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs3756905	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778016	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846871	0.95[ASN][1000 genomes]
rs3957238	0.92[YRI][hapmap]
rs449840	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4594944	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs460539	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4714018	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs58214515	0.96[ASN][1000 genomes]
rs62406643	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6457963	0.88[ASN][1000 genomes]
rs6909988	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910832	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6914008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932175	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs6934844	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7743646	0.80[LWK][hapmap];0.88[YRI][hapmap]
rs7743836	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs7761653	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs7774420	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs831480	0.80[CHB][hapmap]
rs8472	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9296200	0.85[YRI][hapmap]
rs9366920	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9368966	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380610	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs9380616	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9380626	0.86[ASN][1000 genomes]
rs9462233	0.84[AFR][1000 genomes]
rs9462240	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs9462241	0.85[YRI][hapmap]
rs9470426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9380618	GLP1R	cis	parietal	SCAN
rs9380618	LRFN2	cis	cerebellum	SCAN
rs9380618	PNPLA1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36853000-36853600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr6:36853000-36853600	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr6:36853000-36853600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr6:36853000-36853600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr6:36853000-36853600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:36853000-36853600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr6:36853000-36853600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:36853000-36853600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:36853000-36853600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:36853000-36853600	Flanking Active TSS	Liver	Liver
11	chr6:36853000-36853600	Flanking Active TSS	Brain Angular Gyrus	brain
12	chr6:36853000-36853600	Flanking Active TSS	Brain Cingulate Gyrus	brain
13	chr6:36853000-36853600	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr6:36853000-36853600	Flanking Active TSS	Colon Smooth Muscle	Colon
15	chr6:36853000-36853600	Flanking Active TSS	Fetal Intestine Small	intestine
16	chr6:36853000-36853600	Flanking Active TSS	Fetal Kidney	kidney
17	chr6:36853000-36853600	Flanking Active TSS	Rectal Smooth Muscle	rectum
18	chr6:36853000-36853600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr6:36853000-36853600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr6:36853000-36853600	Enhancers	Spleen	Spleen
21	chr6:36853000-36853600	Flanking Active TSS	Dnd41	blood
22	chr6:36853000-36853600	Flanking Active TSS	Hela-S3	cervix
23	chr6:36853000-36853600	Flanking Active TSS	HUVEC	blood vessel
24	chr6:36853000-36853600	Flanking Active TSS	K562	blood
25	chr6:36853000-36853600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:36853000-36855000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:36853200-36853600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
28	chr6:36853200-36853600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:36853200-36853600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:36853200-36853600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:36853200-36853600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr6:36853200-36853600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr6:36853200-36853600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr6:36853200-36853600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:36853200-36853600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:36853200-36853600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr6:36853200-36853600	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr6:36853200-36853600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr6:36853200-36853600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr6:36853200-36853600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr6:36853200-36853600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:36853200-36853600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:36853200-36853600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr6:36853200-36853600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr6:36853200-36853600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr6:36853200-36853600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:36853200-36853600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:36853200-36853600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr6:36853200-36853600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:36853200-36853600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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