Variant report

Variant	rs10672
Chromosome Location	chr6:33662265-33662266
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	MXI1	chr6:33661582-33663177	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:33662091-33663836	K562	blood:	n/a	n/a
3	MYC	chr6:33662027-33662641	HUVEC	blood vessel:	n/a	chr6:33662307-33662316 chr6:33662208-33662216
4	MAX	chr6:33661943-33662575	A549	lung:	n/a	chr6:33662307-33662316 chr6:33662208-33662216
5	POLR2A	chr6:33662045-33662757	HUVEC	blood vessel:	n/a	n/a
6	FOXP2	chr6:33662153-33662586	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr6:33660657-33663799	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:33662254-33662542	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:33661956-33663057	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr6:33662026-33666005	Hela-S3	cervix:	n/a	n/a
11	ZNF263	chr6:33662186-33662597	HEK293-T-REx	kidney:	n/a	n/a
12	POLR2A	chr6:33662069-33664724	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:33662113-33666054	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:33660869-33664890	Hela-S3	cervix:	n/a	n/a
15	MYC	chr6:33662075-33662493	MCF10A-Er-Src	breast:	n/a	chr6:33662307-33662316 chr6:33662208-33662216
16	POLR2A	chr6:33662209-33662538	H1-hESC	embryonic stem cell:	n/a	n/a
17	PBX3	chr6:33661935-33662539	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr6:33662019-33665616	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr6:33657437-33666414	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr6:33662092-33663172	HepG2	liver:	n/a	n/a
21	POLR2A	chr6:33662157-33662345	GM12878	blood:	n/a	n/a
22	REST	chr6:33662080-33662563	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr6:33662094-33663781	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr6:33662064-33662629	HCT-116	colon:	n/a	n/a
25	POLR2A	chr6:33662182-33664245	K562	blood:	n/a	n/a
26	POLR2A	chr6:33662162-33662488	K562	blood:	n/a	n/a
27	MAX	chr6:33662038-33662586	HUVEC	blood vessel:	n/a	chr6:33662307-33662316 chr6:33662208-33662216
28	POLR2A	chr6:33661275-33663273	MCF-7	breast:	n/a	n/a
29	POLR2A	chr6:33662121-33662746	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr6:33662046-33663019	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr6:33662139-33662294	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:33662077-33662648	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr6:33662121-33662782	HCT-116	colon:	n/a	n/a
34	POLR2A	chr6:33662074-33662492	A549	lung:	n/a	n/a
35	POLR2A	chr6:33662027-33662734	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr6:33661893-33662686	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr6:33658911-33667009	K562	blood:	n/a	n/a
38	POLR2A	chr6:33662022-33662440	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr6:33662086-33663570	PFSK-1	brain:	n/a	n/a
40	MAX	chr6:33662072-33662457	SK-N-SH	brain:	n/a	chr6:33662307-33662316 chr6:33662208-33662216
41	SIN3AK20	chr6:33662162-33662591	PFSK-1	brain:	n/a	n/a
42	MYC	chr6:33662065-33662705	MCF10A-Er-Src	breast:	n/a	chr6:33662307-33662316 chr6:33662208-33662216 chr6:33662663-33662672
43	POLR2A	chr6:33662224-33662543	MCF-7	breast:	n/a	n/a
44	POLR2A	chr6:33661569-33663151	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr6:33662149-33663255	PBDE	blood:	n/a	n/a
46	POLR2A	chr6:33661859-33662875	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr6:33662138-33662298	ProgFib	skin:	n/a	n/a
48	POLR2A	chr6:33662135-33662620	HL-60	blood:	n/a	n/a
49	POLR2A	chr6:33658928-33664260	K562	blood:	n/a	n/a
50	POLR2A	chr6:33662098-33662413	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:
2	chr6:33377496..33379251-chr6:33661661..33664420,2	MCF-7	breast:
3	chr6:33599796..33602757-chr6:33660954..33662454,2	MCF-7	breast:

Variant related genes	Relation type
MIR3934	TF binding region
ENSG00000112511	Chromatin interaction
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10947436	1.00[JPT][hapmap]
rs1536501	1.00[JPT][hapmap]
rs1998949	1.00[JPT][hapmap]
rs2182659	1.00[JPT][hapmap]
rs2395401	1.00[JPT][hapmap]
rs2395448	1.00[JPT][hapmap]
rs2967	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap]
rs3818528	0.82[CEU][hapmap];0.81[CHD][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711350	1.00[JPT][hapmap]
rs498114	0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs530614	1.00[JPT][hapmap]
rs545787	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs549652	1.00[JPT][hapmap]
rs597386	1.00[JPT][hapmap]
rs602399	1.00[JPT][hapmap]
rs608971	1.00[JPT][hapmap]
rs623813	1.00[JPT][hapmap]
rs654682	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs658087	1.00[JPT][hapmap]
rs684119	1.00[JPT][hapmap]
rs688209	1.00[JPT][hapmap]
rs6913517	1.00[JPT][hapmap]
rs6915136	1.00[JPT][hapmap]
rs751727	1.00[JPT][hapmap]
rs764753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943463	1.00[JPT][hapmap]
rs943464	1.00[JPT][hapmap]
rs943472	1.00[JPT][hapmap]
rs9461905	1.00[JPT][hapmap]
rs9469542	1.00[JPT][hapmap]

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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10672	LEMD2	cis	cerebellum	SCAN
rs10672	C6orf125	cis	cerebellum	SCAN
rs10672	C6orf227	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33672600	Strong transcription	Dnd41	blood
2	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:33629000-33662800	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:33654800-33662600	Weak transcription	Small Intestine	intestine
12	chr6:33655000-33663600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:33655600-33664800	Weak transcription	Aorta	Aorta
14	chr6:33656400-33662600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:33656400-33666000	Genic enhancers	Spleen	Spleen
16	chr6:33658000-33663400	Genic enhancers	Right Ventricle	heart
17	chr6:33658000-33667200	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr6:33658200-33666600	Genic enhancers	Fetal Muscle Leg	muscle
19	chr6:33658600-33663400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:33658600-33666400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:33658800-33662600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:33659000-33666600	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr6:33659200-33665200	Genic enhancers	HMEC	breast
24	chr6:33659200-33665400	Genic enhancers	NHDF-Ad	bronchial
25	chr6:33659200-33665800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:33659200-33666600	Enhancers	Right Atrium	heart
27	chr6:33659400-33662400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:33659400-33663000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:33659400-33663000	Genic enhancers	NHLF	lung
30	chr6:33659400-33663600	Enhancers	Psoas Muscle	Psoas
31	chr6:33659400-33663800	Enhancers	HSMMtube	muscle
32	chr6:33659400-33664200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr6:33659400-33665000	Genic enhancers	Duodenum Mucosa	Duodenum
34	chr6:33659400-33666400	Genic enhancers	Fetal Thymus	thymus
35	chr6:33659400-33668400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr6:33659600-33662600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:33659600-33662800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:33659600-33663000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr6:33659600-33663600	Enhancers	NH-A	brain
40	chr6:33659600-33664600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:33659600-33665600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:33659600-33666400	Enhancers	Primary hematopoietic stem cells	blood
43	chr6:33659600-33667000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr6:33659800-33662600	Genic enhancers	GM12878-XiMat	blood
45	chr6:33659800-33663200	Genic enhancers	Osteobl	bone
46	chr6:33659800-33664800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:33659800-33665600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:33659800-33666000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr6:33659800-33666600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:33659800-33666600	Genic enhancers	Fetal Stomach	stomach

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