Variant report

Variant	rs6934844
Chromosome Location	chr6:36853309-36853310
allele	C/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	CHD2	chr6:36853186-36853962	Hela-S3	cervix:	n/a	chr6:36853588-36853597
2	REST	chr6:36853054-36854391	H1-neurons	neurons:	n/a	chr6:36853978-36853988 chr6:36853977-36853990
3	ZKSCAN1	chr6:36853282-36853848	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr6:36853248-36853853	K562	blood:	n/a	n/a
5	ARID3A	chr6:36853225-36853830	HepG2	liver:	n/a	n/a
6	POU2F2	chr6:36853242-36853978	GM12878	blood:	n/a	n/a
7	TAF1	chr6:36853252-36853906	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr6:36853253-36853994	HCT-116	colon:	n/a	n/a
9	POLR2A	chr6:36853245-36853993	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:36853153-36854206	GM12892	blood:	n/a	n/a
11	ATF2	chr6:36853255-36853922	GM12878	blood:	n/a	n/a
12	CHD2	chr6:36853239-36854132	K562	blood:	n/a	chr6:36853588-36853597
13	ZNF143	chr6:36853290-36853922	K562	blood:	n/a	n/a
14	CHD2	chr6:36853287-36854104	H1-hESC	embryonic stem cell:	n/a	chr6:36853588-36853597
15	POLR2A	chr6:36853294-36853973	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:36853277-36854069	GM12891	blood:	n/a	n/a
17	EP300	chr6:36853032-36854336	K562	blood:	n/a	n/a
18	RAD21	chr6:36853282-36853792	SK-N-SH_RA	brain:	n/a	chr6:36853552-36853571
19	FOXM1	chr6:36853230-36853897	GM12878	blood:	n/a	n/a
20	SIN3AK20	chr6:36853290-36854165	PANC-1	pancreas:	n/a	n/a
21	NFIC	chr6:36853229-36853920	HepG2	liver:	n/a	n/a
22	STAT5A	chr6:36853176-36854242	GM12878	blood:	n/a	n/a
23	CTCF	chr6:36853307-36853891	K562	blood:	n/a	chr6:36853552-36853568
24	BRCA1	chr6:36853306-36853928	HepG2	liver:	n/a	chr6:36853588-36853597
25	CHD1	chr6:36853303-36853884	GM12878	blood:	n/a	chr6:36853588-36853597
26	RAD21	chr6:36853190-36853968	HCT-116	colon:	n/a	chr6:36853552-36853571
27	ELF1	chr6:36853195-36854132	GM12878	blood:	n/a	chr6:36853701-36853714 chr6:36853722-36853735
28	KAP1	chr6:36853248-36854137	HEK293	kidney:	n/a	n/a
29	NFIC	chr6:36853286-36853934	HepG2	liver:	n/a	n/a
30	CBX3	chr6:36852892-36854233	K562	blood:	n/a	n/a
31	RELA	chr6:36853093-36854031	GM15510	blood:	n/a	n/a
32	TEAD4	chr6:36853177-36854266	K562	blood:	n/a	n/a
33	POLR2A	chr6:36853291-36854187	H1-neurons	neurons:	n/a	n/a
34	SMC3	chr6:36853176-36853778	GM12878	blood:	n/a	chr6:36853553-36853567
35	HCFC1	chr6:36852922-36854602	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr6:36853291-36854092	GM12878	blood:	n/a	n/a
37	ELF1	chr6:36853120-36854249	HCT-116	colon:	n/a	chr6:36853701-36853714 chr6:36853722-36853735
38	MYBL2	chr6:36853153-36854122	HepG2	liver:	n/a	n/a
39	POLR2A	chr6:36853178-36854171	GM12892	blood:	n/a	n/a
40	E2F4	chr6:36853262-36853950	MCF10A-Er-Src	breast:	n/a	chr6:36853769-36853780
41	GTF2F1	chr6:36853298-36853935	H1-hESC	embryonic stem cell:	n/a	n/a
42	GABPA	chr6:36853188-36854234	HL-60	blood:	n/a	n/a
43	POLR2A	chr6:36853289-36854073	GM12892	blood:	n/a	n/a
44	KAP1	chr6:36853175-36853893	U2OS	brain:	n/a	n/a
45	GABPA	chr6:36853254-36854198	MCF-7	breast:	n/a	n/a
46	POLR2A	chr6:36853230-36854023	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr6:36853292-36854269	K562	blood:	n/a	n/a
48	ETS1	chr6:36853301-36854021	A549	lung:	n/a	chr6:36853542-36853549 chr6:36853588-36853597
49	GABPA	chr6:36853257-36854229	A549	lung:	n/a	n/a
50	POLR2A	chr6:36853160-36854189	SK-N-MC	brain:	n/a	n/a

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	chr6:36852138..36856054-chr6:36953606..36956862,5	K562	blood:
7	chr6:36841338..36845965-chr6:36851992..36855231,4	MCF-7	breast:

Variant related genes	Relation type
C6orf89	TF binding region
ENSG00000224086	Chromatin interaction
ENSG00000137168	Chromatin interaction
ENSG00000124772	Chromatin interaction
ENSG00000189167	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000139618	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1022696	0.84[YRI][hapmap]
rs10947647	0.84[YRI][hapmap]
rs1150784	0.88[ASN][1000 genomes]
rs11759850	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs12528273	0.81[JPT][hapmap]
rs2116447	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs2272275	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs2272276	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs2293393	0.89[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2303993	0.98[ASN][1000 genomes]
rs236349	0.81[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs236352	0.94[ASN][1000 genomes]
rs236385	0.89[JPT][hapmap]
rs236386	0.89[JPT][hapmap]
rs2395663	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs3756905	0.98[ASN][1000 genomes]
rs3778016	0.98[ASN][1000 genomes]
rs3778017	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3846871	0.93[ASN][1000 genomes]
rs3957238	0.92[YRI][hapmap]
rs449840	0.92[ASN][1000 genomes]
rs460539	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4711471	0.85[EUR][1000 genomes]
rs4711473	0.81[AFR][1000 genomes]
rs4714018	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58214515	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62406643	0.94[ASN][1000 genomes]
rs6457963	0.85[ASN][1000 genomes]
rs6909988	0.98[ASN][1000 genomes]
rs6910832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914008	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6932175	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs7743646	0.83[LWK][hapmap];0.88[YRI][hapmap]
rs7743836	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs7761653	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs7774420	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs831480	0.86[CHB][hapmap]
rs8472	0.88[ASN][1000 genomes]
rs9296200	0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs9349017	0.88[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs9366920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368966	0.96[ASN][1000 genomes]
rs9380616	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380618	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]
rs9380626	0.84[ASN][1000 genomes]
rs9462238	0.80[AFR][1000 genomes]
rs9462240	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs9462241	0.84[YRI][hapmap]
rs9470426	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6934844	TCP11	cis	cerebellum	SCAN
rs6934844	LRFN2	cis	cerebellum	SCAN
rs6934844	STK38	cis	cerebellum	SCAN
rs6934844	PNPLA1	cis	parietal	SCAN
rs6934844	SRPK1	cis	cerebellum	SCAN
rs6934844	SPDEF	cis	parietal	SCAN
rs6934844	PPIL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36853000-36853400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr6:36853000-36853400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:36853000-36853400	Flanking Active TSS	Brain Anterior Caudate	brain
4	chr6:36853000-36853400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
5	chr6:36853000-36853400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:36853000-36853400	Enhancers	Esophagus	oesophagus
7	chr6:36853000-36853400	Flanking Active TSS	Fetal Brain Female	brain
8	chr6:36853000-36853400	Enhancers	Gastric	stomach
9	chr6:36853000-36853400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr6:36853000-36853400	Enhancers	Stomach Mucosa	stomach
11	chr6:36853000-36853400	Enhancers	Thymus	Thymus
12	chr6:36853000-36853400	Flanking Active TSS	GM12878-XiMat	blood
13	chr6:36853000-36853400	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr6:36853000-36853600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr6:36853000-36853600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr6:36853000-36853600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr6:36853000-36853600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr6:36853000-36853600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:36853000-36853600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr6:36853000-36853600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:36853000-36853600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:36853000-36853600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:36853000-36853600	Flanking Active TSS	Liver	Liver
24	chr6:36853000-36853600	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr6:36853000-36853600	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr6:36853000-36853600	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr6:36853000-36853600	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr6:36853000-36853600	Flanking Active TSS	Fetal Intestine Small	intestine
29	chr6:36853000-36853600	Flanking Active TSS	Fetal Kidney	kidney
30	chr6:36853000-36853600	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr6:36853000-36853600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr6:36853000-36853600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr6:36853000-36853600	Enhancers	Spleen	Spleen
34	chr6:36853000-36853600	Flanking Active TSS	Dnd41	blood
35	chr6:36853000-36853600	Flanking Active TSS	Hela-S3	cervix
36	chr6:36853000-36853600	Flanking Active TSS	HUVEC	blood vessel
37	chr6:36853000-36853600	Flanking Active TSS	K562	blood
38	chr6:36853000-36853600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr6:36853000-36855000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:36853200-36853400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:36853200-36853400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:36853200-36853400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:36853200-36853400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:36853200-36853400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:36853200-36853400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:36853200-36853400	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr6:36853200-36853400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr6:36853200-36853400	Flanking Active TSS	Fetal Heart	heart
49	chr6:36853200-36853400	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr6:36853200-36853400	Flanking Active TSS	Fetal Lung	lung

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