Variant report

Variant	rs3804317
Chromosome Location	chr6:4135342-4135343
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	chr6:4135164-4136590	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:4135161-4136663	Hela-S3	cervix:	n/a	n/a
3	MYC	chr6:4135055-4136536	NB4	blood:	n/a	chr6:4136289-4136298
4	SMC3	chr6:4135188-4135697	Hela-S3	cervix:	n/a	n/a
5	E2F6	chr6:4135195-4135584	K562	blood:	n/a	n/a
6	MXI1	chr6:4135218-4135637	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:4135231-4135844	HUVEC	blood vessel:	n/a	n/a
8	SIN3A	chr6:4134395-4135873	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:4135313-4136599	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr6:4135298-4135857	K562	blood:	n/a	n/a
11	MXI1	chr6:4135200-4135795	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:4135201-4135816	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:4135079-4136590	HepG2	liver:	n/a	n/a
14	HCFC1	chr6:4135261-4135818	K562	blood:	n/a	n/a
15	POLR2A	chr6:4135213-4136014	H1-neurons	neurons:	n/a	n/a
16	CREB1	chr6:4135140-4135885	H1-hESC	embryonic stem cell:	n/a	n/a
17	SMC3	chr6:4135302-4135736	K562	blood:	n/a	n/a
18	TBP	chr6:4135143-4136710	K562	blood:	n/a	n/a
19	MAX	chr6:4135106-4135796	K562	blood:	n/a	n/a
20	IRF1	chr6:4134975-4135835	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
21	KAP1	chr6:4135202-4135704	HEK293	kidney:	n/a	n/a
22	POLR2A	chr6:4134214-4135809	PBDE	blood:	n/a	n/a
23	IRF1	chr6:4135158-4136680	K562	blood:	n/a	chr6:4135177-4135190 chr6:4135178-4135192 chr6:4135178-4135190 chr6:4135178-4135191 chr6:4135178-4135191 chr6:4135179-4135193 chr6:4135178-4135189 chr6:4135177-4135197 chr6:4135178-4135191 chr6:4135178-4135191
24	HMGN3	chr6:4135260-4136604	K562	blood:	n/a	n/a
25	POLR2A	chr6:4135168-4136541	GM19099	blood:	n/a	n/a
26	YY1	chr6:4135190-4135848	H1-hESC	embryonic stem cell:	n/a	n/a
27	SIN3AK20	chr6:4135319-4135575	HepG2	liver:	n/a	n/a
28	TCF7L2	chr6:4135202-4135737	Hela-S3	cervix:	n/a	n/a
29	MAX	chr6:4135071-4135858	SK-N-SH	brain:	n/a	n/a
30	BHLHE40	chr6:4134431-4135779	GM12878	blood:	n/a	n/a
31	CHD2	chr6:4135163-4136550	Hela-S3	cervix:	n/a	chr6:4136253-4136263
32	RCOR1	chr6:4135279-4135816	HepG2	liver:	n/a	n/a
33	GTF2B	chr6:4135280-4135806	K562	blood:	n/a	n/a
34	MAX	chr6:4135318-4135860	ECC-1	luminal epithelium:	n/a	n/a
35	MAX	chr6:4135093-4135857	H1-hESC	embryonic stem cell:	n/a	n/a
36	REST	chr6:4135182-4135769	A549	lung:	n/a	n/a
37	POLR2A	chr6:4135067-4136561	GM15510	blood:	n/a	n/a
38	YY1	chr6:4135127-4135853	SK-N-SH	brain:	n/a	n/a
39	JUND	chr6:4135202-4135820	K562	blood:	n/a	n/a
40	POLR2A	chr6:4134212-4135928	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:4135138-4135861	GM12892	blood:	n/a	n/a
42	POLR2A	chr6:4135153-4135946	GM12878	blood:	n/a	n/a
43	YY1	chr6:4135271-4136616	HepG2	liver:	n/a	n/a
44	MTA3	chr6:4135055-4135838	GM12878	blood:	n/a	n/a
45	MAX	chr6:4135180-4135515	A549	lung:	n/a	n/a
46	POLR2A	chr6:4135212-4135844	PFSK-1	brain:	n/a	n/a
47	MYC	chr6:4135290-4135372	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr6:4135086-4136004	K562	blood:	n/a	n/a
49	MBD4	chr6:4135277-4135807	HepG2	liver:	n/a	n/a
50	CHD2	chr6:4135177-4135502	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4134858..4135600-chr6:74230356..74231112,2	Hela-S3	cervix:
2	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
3	chr5:180672773..180673634-chr6:4135301..4135859,2	Hela-S3	cervix:
4	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:

Variant related genes	Relation type
ENSG00000254821	TF binding region
ECI2	TF binding region
ENSG00000234817	TF binding region
ENSG00000272248	Chromatin interaction
ENSG00000233937	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000230648	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11751668	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11753305	0.87[ASN][1000 genomes]
rs11754487	0.86[ASN][1000 genomes]
rs11754986	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789215	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812186	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4443542	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6916172	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932036	0.85[ASN][1000 genomes]
rs6935587	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378841	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378842	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378843	0.85[ASN][1000 genomes]
rs9392552	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392554	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9392555	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392556	0.85[ASN][1000 genomes]
rs9405220	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9405221	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9405702	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9503933	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9503934	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503936	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	esv3413228	chr6:4134778-4137526	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv3369872	chr6:4134903-4137401	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4133800-4136800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:4133800-4136800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:4134000-4135600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:4134000-4136800	Active TSS	Ovary	ovary
5	chr6:4134000-4136800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:4134200-4135400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:4134200-4135800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr6:4134200-4136800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:4134200-4136800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:4134200-4137000	Active TSS	Aorta	Aorta
11	chr6:4134400-4135400	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr6:4134400-4136600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr6:4134400-4136600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:4134400-4136600	Active TSS	Fetal Brain Female	brain
15	chr6:4134400-4136600	Active TSS	Hela-S3	cervix
16	chr6:4134400-4136800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:4134400-4137000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:4134600-4135400	Active TSS	Right Atrium	heart
19	chr6:4134600-4135600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr6:4134600-4136400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:4134600-4136400	Active TSS	Fetal Intestine Large	intestine
22	chr6:4134600-4136400	Active TSS	HSMM	muscle
23	chr6:4134600-4136400	Active TSS	K562	blood
24	chr6:4134600-4136600	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr6:4134600-4136600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:4134600-4136600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:4134600-4136600	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr6:4134600-4136600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:4134600-4136600	Active TSS	Gastric	stomach
30	chr6:4134600-4136600	Bivalent/Poised TSS	HepG2	liver
31	chr6:4134600-4136600	Active TSS	HSMMtube	muscle
32	chr6:4134600-4136800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr6:4134600-4136800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:4134600-4136800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:4134600-4136800	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr6:4134600-4136800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:4134600-4136800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:4134600-4136800	Active TSS	Brain Anterior Caudate	brain
39	chr6:4134600-4136800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr6:4134600-4136800	Active TSS	Esophagus	oesophagus
41	chr6:4134600-4136800	Active TSS	Right Ventricle	heart
42	chr6:4134600-4136800	Active TSS	A549	lung
43	chr6:4134600-4136800	Active TSS	NHDF-Ad	bronchial
44	chr6:4134600-4137000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:4134600-4137000	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:4134800-4135800	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr6:4134800-4136400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:4134800-4136400	Active TSS	Primary T cells fromperipheralblood	blood
49	chr6:4134800-4136400	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr6:4134800-4136400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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