Variant report

Variant	rs4707842
Chromosome Location	chr6:71378313-71378314
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	POLR2A	chr6:71376772-71378355	GM12892	blood:	n/a	n/a
2	MXI1	chr6:71377057-71378418	Hela-S3	cervix:	n/a	n/a
3	E2F4	chr6:71377269-71378419	K562	blood:	n/a	chr6:71377411-71377420 chr6:71377988-71377997 chr6:71377640-71377650 chr6:71378159-71378174
4	POLR2A	chr6:71377203-71378349	GM10847	blood:	n/a	n/a
5	POLR2A	chr6:71377220-71378526	IMR90	lung:	n/a	n/a
6	POLR2A	chr6:71377168-71378330	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:71377916-71378417	HCT-116	colon:	n/a	n/a
8	RCOR1	chr6:71378245-71378324	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:71377129-71378340	GM18526	blood:	n/a	n/a
10	MXI1	chr6:71377009-71378379	HepG2	liver:	n/a	n/a
11	SMC3	chr6:71378116-71378371	Hela-S3	cervix:	n/a	n/a
12	TBP	chr6:71377126-71378396	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD2	chr6:71378081-71378373	K562	blood:	n/a	n/a
14	YY1	chr6:71377105-71378331	H1-hESC	embryonic stem cell:	n/a	chr6:71377639-71377653 chr6:71377979-71377993 chr6:71377675-71377689 chr6:71377683-71377692 chr6:71377902-71377913 chr6:71377627-71377641 chr6:71378027-71378036
15	SMARCB1	chr6:71377119-71378432	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr6:71376982-71378452	IMR90	lung:	n/a	n/a
17	MTA3	chr6:71376710-71378399	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:71376668-71378316	Raji	blood:	n/a	n/a
19	POLR2A	chr6:71377144-71378386	H1-hESC	embryonic stem cell:	n/a	n/a
20	BHLHE40	chr6:71377037-71378388	GM12878	blood:	n/a	chr6:71377674-71377690
21	POLR2A	chr6:71376812-71378459	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr6:71377192-71378336	MCF-7	breast:	n/a	n/a
23	BACH1	chr6:71378165-71378411	H1-hESC	embryonic stem cell:	n/a	n/a
24	MYC	chr6:71378136-71378389	K562	blood:	n/a	n/a
25	POLR2A	chr6:71377147-71378356	MCF-7	breast:	n/a	n/a
26	POLR2A	chr6:71377014-71378376	GM12892	blood:	n/a	n/a
27	ZNF263	chr6:71377133-71378652	HEK293-T-REx	kidney:	n/a	chr6:71378076-71378085
28	POLR2A	chr6:71377116-71378360	H1-neurons	neurons:	n/a	n/a
29	RCOR1	chr6:71376942-71378400	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr6:71377139-71378348	HUVEC	blood vessel:	n/a	n/a
31	ZEB1	chr6:71377994-71378405	GM12878	blood:	n/a	n/a
32	CHD2	chr6:71377159-71378417	Hela-S3	cervix:	n/a	chr6:71377707-71377717
33	HEY1	chr6:71378066-71378446	HepG2	liver:	n/a	n/a
34	ZNF143	chr6:71377880-71378329	H1-hESC	embryonic stem cell:	n/a	chr6:71377988-71377998
35	POLR2A	chr6:71377126-71378339	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:71377042-71378394	PBDE	blood:	n/a	n/a
37	POLR2A	chr6:71376984-71378489	H1-hESC	embryonic stem cell:	n/a	n/a
38	SIN3A	chr6:71377295-71378543	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr6:71377144-71378391	HepG2	liver:	n/a	n/a
40	TAF1	chr6:71377085-71378416	H1-hESC	embryonic stem cell:	n/a	n/a
41	TCF7L2	chr6:71377223-71378426	Hela-S3	cervix:	n/a	chr6:71378372-71378386
42	MAX	chr6:71377037-71378352	GM12878	blood:	n/a	n/a
43	MAFK	chr6:71378151-71378331	Hela-S3	cervix:	n/a	chr6:71378288-71378303
44	POLR2A	chr6:71378194-71378687	MCF10A-Er-Src	breast:	n/a	n/a
45	CTCF	chr6:71378220-71378370	HPAF	blood vessel:	n/a	n/a
46	MAX	chr6:71377098-71378353	HepG2	liver:	n/a	n/a
47	KAP1	chr6:71376867-71378495	HEK293	kidney:	n/a	n/a
48	ZBTB7A	chr6:71377799-71378350	K562	blood:	n/a	n/a
49	POLR2A	chr6:71377077-71378318	NB4	blood:	n/a	n/a
50	SMARCC1	chr6:71377071-71378400	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:71276528..71278152-chr6:71377519..71380132,3	MCF-7	breast:
2	chr6:71103256..71105709-chr6:71376472..71378763,2	K562	blood:
3	chr6:71275419..71277021-chr6:71378291..71380328,2	K562	blood:
4	chr6:71377896..71380271-chr6:71393211..71395433,2	K562	blood:
5	chr5:71603686..71604329-chr6:71377716..71378702,2	Hela-S3	cervix:
6	chr6:71372618..71374735-chr6:71377886..71379472,2	MCF-7	breast:
7	chr6:71275193..71277991-chr6:71376243..71378994,4	MCF-7	breast:

Variant related genes	Relation type
SLC25A6P6	TF binding region
ENSG00000237643	Chromatin interaction
ENSG00000154079	Chromatin interaction
ENSG00000218870	Chromatin interaction
ENSG00000113048	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2274972	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3734369	0.97[EUR][1000 genomes]
rs4706460	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707844	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61001507	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6902786	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6919104	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6940971	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6941789	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7747310	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7748778	0.97[EUR][1000 genomes]
rs7754217	0.87[AFR][1000 genomes]
rs7764445	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9342795	0.81[AFR][1000 genomes]
rs9342796	1.00[EUR][1000 genomes]
rs9346403	0.92[EUR][1000 genomes]
rs9351793	0.87[AFR][1000 genomes]
rs9354937	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9354938	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9360426	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9364102	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9364103	0.87[AFR][1000 genomes]
rs9364109	0.92[EUR][1000 genomes]
rs9364111	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS 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	29 gene(s)	inside rSNPs	diseases
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr6:71376600-71378400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:71376600-71378800	Active TSS	HSMMtube	muscle
3	chr6:71376600-71379400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr6:71376800-71378600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:71376800-71378800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr6:71376800-71378800	Active TSS	Fetal Muscle Trunk	muscle
7	chr6:71376800-71379000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:71376800-71379000	Active TSS	Rectal Smooth Muscle	rectum
9	chr6:71376800-71379200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:71376800-71379200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:71376800-71379200	Active TSS	A549	lung
12	chr6:71377000-71378400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:71377000-71378400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:71377000-71378400	Active TSS	Brain Angular Gyrus	brain
15	chr6:71377000-71378400	Active TSS	Brain Hippocampus Middle	brain
16	chr6:71377000-71378400	Active TSS	Colon Smooth Muscle	Colon
17	chr6:71377000-71378600	Active TSS	Aorta	Aorta
18	chr6:71377000-71378600	Active TSS	Fetal Brain Male	brain
19	chr6:71377000-71378600	Active TSS	Left Ventricle	heart
20	chr6:71377000-71378600	Active TSS	Ovary	ovary
21	chr6:71377000-71378800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr6:71377000-71378800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:71377000-71378800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr6:71377000-71378800	Active TSS	HSMM	muscle
25	chr6:71377000-71379000	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr6:71377000-71379000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:71377000-71379000	Active TSS	Fetal Muscle Leg	muscle
28	chr6:71377000-71379000	Active TSS	NHDF-Ad	bronchial
29	chr6:71377000-71379200	Active TSS	Psoas Muscle	Psoas
30	chr6:71377000-71379400	Active TSS	Colonic Mucosa	Colon
31	chr6:71377000-71379400	Active TSS	Right Atrium	heart
32	chr6:71377200-71378400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:71377200-71378400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:71377200-71378400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:71377200-71378400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr6:71377200-71378400	Active TSS	Muscle Satellite Cultured Cells	--
37	chr6:71377200-71378400	Active TSS	Brain Anterior Caudate	brain
38	chr6:71377200-71378400	Active TSS	Esophagus	oesophagus
39	chr6:71377200-71378400	Active TSS	Fetal Kidney	kidney
40	chr6:71377200-71378400	Active TSS	Lung	lung
41	chr6:71377200-71378400	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr6:71377200-71378400	Active TSS	Small Intestine	intestine
43	chr6:71377200-71378600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:71377200-71378600	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr6:71377200-71378600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:71377200-71378600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:71377200-71378600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:71377200-71378600	Active TSS	Placenta	Placenta
49	chr6:71377200-71378800	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr6:71377200-71378800	Active TSS	iPS-15b Cell Line	embryonic stem cell

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