Variant report

Variant	rs627902
Chromosome Location	chr6:4134497-4134498
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	TBP	chr6:4134308-4134909	K562	blood:	n/a	n/a
2	TAF1	chr6:4134215-4134784	K562	blood:	n/a	n/a
3	SIN3A	chr6:4134395-4135873	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr6:4134467-4134796	K562	blood:	n/a	n/a
5	POLR2A	chr6:4134214-4135809	PBDE	blood:	n/a	n/a
6	BHLHE40	chr6:4134279-4134930	K562	blood:	n/a	n/a
7	BHLHE40	chr6:4134431-4135779	GM12878	blood:	n/a	n/a
8	MAX	chr6:4134254-4134851	K562	blood:	n/a	n/a
9	EGR1	chr6:4134482-4134880	K562	blood:	n/a	chr6:4134684-4134697 chr6:4134685-4134699 chr6:4134684-4134697 chr6:4134649-4134658 chr6:4134687-4134696
10	POLR2A	chr6:4134212-4135928	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:4134462-4134755	K562	blood:	n/a	n/a
12	MYC	chr6:4134405-4134896	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:4134490-4134525	ProgFib	skin:	n/a	n/a
14	MAZ	chr6:4134257-4134886	K562	blood:	n/a	n/a
15	MYC	chr6:4134276-4136820	K562	blood:	n/a	chr6:4136289-4136298
16	MAX	chr6:4134405-4134852	Hela-S3	cervix:	n/a	n/a
17	RFX5	chr6:4134307-4135793	Hela-S3	cervix:	n/a	chr6:4135632-4135640
18	POLR2A	chr6:4134238-4135044	HepG2	liver:	n/a	n/a
19	MXI1	chr6:4134305-4135808	GM12878	blood:	n/a	n/a
20	TBL1XR1	chr6:4134263-4135720	K562	blood:	n/a	n/a
21	TEAD4	chr6:4134014-4135039	K562	blood:	n/a	n/a
22	POU2F2	chr6:4134423-4134696	GM12891	blood:	n/a	chr6:4134463-4134476 chr6:4134462-4134483
23	CUX1	chr6:4134196-4134557	K562	blood:	n/a	n/a
24	MYBL2	chr6:4134059-4134979	HepG2	liver:	n/a	n/a
25	UBTF	chr6:4134393-4134789	K562	blood:	n/a	n/a
26	TAL1	chr6:4134165-4134602	K562	blood:	n/a	n/a
27	POLR2A	chr6:4134256-4136602	Hela-S3	cervix:	n/a	n/a
28	HEY1	chr6:4134207-4134847	K562	blood:	n/a	n/a
29	CBX3	chr6:4134169-4134920	K562	blood:	n/a	chr6:4134467-4134478
30	MAX	chr6:4134470-4134802	GM12878	blood:	n/a	n/a
31	IRF1	chr6:4133973-4135818	K562	blood:	n/a	chr6:4135177-4135190 chr6:4134990-4135001 chr6:4135178-4135192 chr6:4134988-4135001 chr6:4135178-4135190 chr6:4135178-4135191 chr6:4135178-4135191 chr6:4135179-4135193 chr6:4135178-4135189 chr6:4134988-4135001 chr6:4135177-4135197 chr6:4135178-4135191 chr6:4135178-4135191 chr6:4134936-4134952
32	EGR1	chr6:4134479-4134821	K562	blood:	n/a	chr6:4134684-4134697 chr6:4134685-4134699 chr6:4134684-4134697 chr6:4134649-4134658 chr6:4134687-4134696
33	YY1	chr6:4134459-4134824	K562	blood:	n/a	chr6:4134732-4134748
34	NFIC	chr6:4134261-4134925	HepG2	liver:	n/a	n/a
35	TBP	chr6:4134224-4135796	Hela-S3	cervix:	n/a	n/a
36	MAZ	chr6:4134311-4134898	GM12878	blood:	n/a	n/a
37	UBTF	chr6:4134026-4135847	K562	blood:	n/a	n/a
38	HNF4G	chr6:4134118-4134962	HepG2	liver:	n/a	chr6:4134876-4134890 chr6:4134292-4134310 chr6:4134881-4134889 chr6:4134295-4134307 chr6:4134295-4134307 chr6:4134875-4134890
39	POLR2A	chr6:4134403-4134640	HepG2	liver:	n/a	n/a
40	MYC	chr6:4134097-4136687	K562	blood:	n/a	chr6:4136289-4136298
41	GTF2F1	chr6:4134207-4134748	Hela-S3	cervix:	n/a	n/a
42	MAX	chr6:4134156-4134876	K562	blood:	n/a	n/a
43	POLR2A	chr6:4134446-4134806	Hela-S3	cervix:	n/a	n/a
44	TEAD4	chr6:4134263-4134731	H1-hESC	embryonic stem cell:	n/a	n/a
45	CHD2	chr6:4134242-4134844	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr6:4134153-4134906	K562	blood:	n/a	n/a
47	POLR2A	chr6:4134479-4134523	K562	blood:	n/a	n/a
48	RFX5	chr6:4133781-4134646	HepG2	liver:	n/a	n/a
49	MAX	chr6:4134439-4134826	K562	blood:	n/a	n/a
50	YY1	chr6:4134459-4134892	K562	blood:	n/a	chr6:4134732-4134748

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:4134485-4134535	RPTEC	kidney:	n/a
2	chr6:4134485-4134535	CMK	blood:	n/a
3	chr6:4134485-4134535	MCF-7	breast:	n/a
4	chr6:4134485-4134535	H1-hESC	embryonic stem cell:	embryo
5	chr6:4134485-4134535	NB4	blood:	n/a
6	chr6:4134485-4134535	IMR90	lung:	fetal
7	chr6:4134485-4134535	BJ	skin:	n/a
8	chr6:4134485-4134535	PFSK-1	brain:	n/a
9	chr6:4134485-4134535	GM12891	blood:	n/a
10	chr6:4134485-4134535	HUVEC	blood vessel:	n/a
11	chr6:4134485-4134535	SK-N-SH	brain:	n/a
12	chr6:4134485-4134535	AG04449	skin:	fetal
13	chr6:4134485-4134535	LNCaP	prostate:	n/a
14	chr6:4134485-4134535	GM06990	blood:	n/a
15	chr6:4134485-4134535	SKMC	muscle:	n/a
16	chr6:4134485-4134535	Hepatocyte	liver:	n/a
17	chr6:4134485-4134535	HCT-116	colon:	n/a
18	chr6:4134485-4134535	HEK293	kidney:	embryo
19	chr6:4134485-4134535	HIPEpiC	eye:	n/a
20	chr6:4134485-4134535	Caco-2	colon:	n/a
21	chr6:4134485-4134535	HRE	kidney:	n/a
22	chr6:4134485-4134535	Jurkat	blood:	n/a
23	chr6:4134485-4134535	HNPCEpiC	eye:	n/a
24	chr6:4134485-4134535	PANC-1	pancreas:	n/a
25	chr6:4134485-4134535	NT2-D1	testis:	n/a
26	chr6:4134485-4134535	U87	brain:	n/a
27	chr6:4134485-4134535	SAEC	small airway:	n/a
28	chr6:4134485-4134535	A549	lung:	n/a
29	chr6:4134485-4134535	HCPEpiC	choroid plexus:	n/a
30	chr6:4134485-4134535	Hela-S3	cervix:	n/a
31	chr6:4134485-4134535	HRCEpiC	kidney:	n/a
32	chr6:4134485-4134535	GM12892	blood:	n/a
33	chr6:4134485-4134535	NHBE	bronchial:	n/a
34	chr6:4134485-4134535	HepG2	liver:	n/a
35	chr6:4134485-4134535	ECC-1	luminal epithelium:	n/a
36	chr6:4134485-4134535	SK-N-MC	brain:	n/a
37	chr6:4134485-4134535	NH-A	brain:	n/a
38	chr6:4134485-4134535	HRPEpiC	eye:	n/a
39	chr6:4134485-4134535	AoSMC	blood vessel:	n/a
40	chr6:4134485-4134535	T-47D	breast:	n/a
41	chr6:4134485-4134535	K562	blood:	n/a
42	chr6:4134485-4134535	HCM	heart:	n/a
43	chr6:4134485-4134535	AG09309	skin:	n/a
44	chr6:4134485-4134535	HEEpiC	esophagus:	n/a
45	chr6:4134485-4134535	SK-N-SH_RA	brain:	n/a
46	chr6:4134485-4134535	PrEC	prostate:	n/a
47	chr6:4134485-4134535	HMEC	breast:	n/a
48	chr6:4134485-4134535	GM19239	blood:	n/a
49	chr6:4134485-4134535	AG09319	gingival:	n/a
50	chr6:4134485-4134535	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr6:4056059..4057941-chr6:4133460..4135296,2	K562	blood:
2	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
3	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-5	chr6:4131253-4134818	NONHSAT107321

Variant related genes	Relation type
ECI2	TF binding region
ENSG00000234817	TF binding region
ENSG00000254821	TF binding region
ENSG00000254821	CpG island
ENSG00000234817	CpG island
ECI2	CpG island
ENSG00000112739	Chromatin interaction
ENSG00000272248	Chromatin interaction
ENSG00000230648	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10085196	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1204950	0.93[ASN][1000 genomes]
rs13205642	0.89[EUR][1000 genomes]
rs13206444	0.89[EUR][1000 genomes]
rs13210282	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2326407	0.89[EUR][1000 genomes]
rs34094324	0.89[EUR][1000 genomes]
rs34200917	0.89[EUR][1000 genomes]
rs605301	1.00[ASN][1000 genomes]
rs608917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611677	0.95[ASN][1000 genomes]
rs622859	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625577	1.00[ASN][1000 genomes]
rs629533	1.00[ASN][1000 genomes]
rs633677	1.00[ASN][1000 genomes]
rs656694	1.00[ASN][1000 genomes]
rs6597030	0.89[EUR][1000 genomes]
rs715165	0.81[EUR][1000 genomes]
rs71553906	0.89[EUR][1000 genomes]
rs7742642	0.84[EUR][1000 genomes]
rs853412	0.98[ASN][1000 genomes]
rs853421	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853422	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328222	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs945251	0.93[ASN][1000 genomes]
rs9689605	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4113800-4134600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:4133200-4134800	Flanking Active TSS	Liver	Liver
3	chr6:4133600-4134600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:4133600-4134600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:4133600-4134800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:4133600-4134800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr6:4133600-4134800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr6:4133800-4134600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:4133800-4134600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:4133800-4134600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr6:4133800-4134600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:4133800-4134600	Enhancers	Fetal Heart	heart
13	chr6:4133800-4134600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr6:4133800-4134600	Enhancers	Spleen	Spleen
15	chr6:4133800-4134600	Transcr. at gene 5' and 3'	HepG2	liver
16	chr6:4133800-4134600	Flanking Active TSS	Osteobl	bone
17	chr6:4133800-4134800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:4133800-4134800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:4133800-4134800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:4133800-4134800	Flanking Active TSS	NHLF	lung
21	chr6:4133800-4135000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:4133800-4135000	Flanking Active TSS	HUVEC	blood vessel
23	chr6:4133800-4136800	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:4133800-4136800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr6:4134000-4134600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr6:4134000-4134600	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr6:4134000-4134600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr6:4134000-4134600	Flanking Active TSS	K562	blood
29	chr6:4134000-4134600	Flanking Active TSS	NHDF-Ad	bronchial
30	chr6:4134000-4135000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr6:4134000-4135000	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr6:4134000-4135000	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr6:4134000-4135000	Flanking Active TSS	Dnd41	blood
34	chr6:4134000-4135000	Flanking Active TSS	NH-A	brain
35	chr6:4134000-4135200	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr6:4134000-4135600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:4134000-4136800	Active TSS	Ovary	ovary
38	chr6:4134000-4136800	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr6:4134200-4134600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr6:4134200-4134600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr6:4134200-4134600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr6:4134200-4134600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:4134200-4134600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr6:4134200-4134600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr6:4134200-4134600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:4134200-4134600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr6:4134200-4134600	Flanking Active TSS	Fetal Kidney	kidney
48	chr6:4134200-4134600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr6:4134200-4134600	Enhancers	Fetal Muscle Leg	muscle
50	chr6:4134200-4134600	Enhancers	Fetal Thymus	thymus

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