Variant report

Variant	rs10946695
Chromosome Location	chr6:24402889-24402890
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	MAX	chr6:24402713-24404074	HepG2	liver:	n/a	n/a
2	REST	chr6:24402834-24403795	HepG2	liver:	n/a	chr6:24403613-24403626
3	RCOR1	chr6:24402864-24403974	K562	blood:	n/a	n/a
4	TAF1	chr6:24402880-24403565	A549	lung:	n/a	n/a
5	POLR2A	chr6:24402881-24403691	K562	blood:	n/a	n/a
6	HDAC2	chr6:24402813-24403286	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr6:24402880-24403849	K562	blood:	n/a	n/a
8	POLR2A	chr6:24402874-24403843	Hela-S3	cervix:	n/a	n/a
9	HA-E2F1	chr6:24402846-24403826	MCF-7	breast:	n/a	chr6:24403131-24403141 chr6:24403129-24403138
10	PML	chr6:24402870-24403571	GM12878	blood:	n/a	n/a
11	RFX5	chr6:24402813-24403848	HepG2	liver:	n/a	chr6:24403729-24403746 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403476-24403485 chr6:24403473-24403488
12	MAFK	chr6:24402649-24403438	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:24402864-24403443	SK-N-SH	brain:	n/a	n/a
14	ZEB1	chr6:24402869-24403333	GM12878	blood:	n/a	chr6:24403031-24403042
15	TEAD4	chr6:24402763-24403289	A549	lung:	n/a	n/a
16	FOS	chr6:24402883-24403066	MCF10A-Er-Src	breast:	n/a	n/a
17	REST	chr6:24402855-24403512	K562	blood:	n/a	n/a
18	RFX5	chr6:24402643-24403772	Hela-S3	cervix:	n/a	chr6:24403729-24403746 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403476-24403485 chr6:24403473-24403488
19	HEY1	chr6:24402843-24403839	HepG2	liver:	n/a	chr6:24403144-24403159
20	POLR2A	chr6:24402862-24403772	Gliobla	brain:	n/a	n/a
21	POLR2A	chr6:24402715-24403861	PFSK-1	brain:	n/a	n/a
22	MXI1	chr6:24402580-24404065	IMR90	lung:	n/a	n/a
23	POLR2A	chr6:24402840-24403789	ECC-1	luminal epithelium:	n/a	n/a
24	SIN3AK20	chr6:24402800-24403972	MCF-7	breast:	n/a	n/a
25	POLR2A	chr6:24402815-24403828	HepG2	liver:	n/a	n/a
26	REST	chr6:24402781-24403098	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:24402710-24403983	SK-N-MC	brain:	n/a	n/a
28	MAX	chr6:24402823-24403964	K562	blood:	n/a	n/a
29	TBP	chr6:24402886-24403382	Hela-S3	cervix:	n/a	n/a
30	TAF1	chr6:24402878-24403809	ECC-1	luminal epithelium:	n/a	n/a
31	ZEB1	chr6:24402832-24403494	GM12878	blood:	n/a	chr6:24403031-24403042
32	POLR2A	chr6:24402844-24403753	MCF-7	breast:	n/a	n/a
33	TCF12	chr6:24402849-24403614	ECC-1	luminal epithelium:	n/a	n/a
34	SP1	chr6:24402868-24403466	A549	lung:	n/a	n/a
35	POLR2A	chr6:24402875-24403755	GM15510	blood:	n/a	n/a
36	CHD1	chr6:24402666-24403634	H1-hESC	embryonic stem cell:	n/a	n/a
37	NR2F2	chr6:24402887-24403760	MCF-7	breast:	n/a	n/a
38	NFIC	chr6:24402879-24403613	HepG2	liver:	n/a	n/a
39	POLR2A	chr6:24402889-24403553	PFSK-1	brain:	n/a	n/a
40	FOXA1	chr6:24402872-24403317	HepG2	liver:	n/a	n/a
41	REST	chr6:24402723-24403242	ECC-1	luminal epithelium:	n/a	n/a
42	MAX	chr6:24402851-24403874	H1-hESC	embryonic stem cell:	n/a	n/a
43	FOXA1	chr6:24402878-24403254	T-47D	breast:	n/a	n/a
44	POLR2A	chr6:24402801-24403468	HCT-116	colon:	n/a	n/a
45	MXI1	chr6:24402781-24404088	K562	blood:	n/a	n/a
46	POLR2A	chr6:24402873-24403571	GM12892	blood:	n/a	n/a
47	ZEB1	chr6:24402209-24403982	HepG2	liver:	n/a	chr6:24403031-24403042
48	MYC	chr6:24402866-24403281	MCF10A-Er-Src	breast:	n/a	n/a
49	MAX	chr6:24402798-24403975	H1-hESC	embryonic stem cell:	n/a	n/a
50	GTF2F1	chr6:24402809-24403929	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24401784..24404907-chr6:24494976..24497958,4	MCF-7	breast:

Variant related genes	Relation type
MRS2	TF binding region
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10946696	0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs1321818	0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6899605	1.00[EUR][1000 genomes]
rs7449704	1.00[EUR][1000 genomes]
rs9467138	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24401200-24403000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:24401200-24403000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:24401800-24403000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:24401800-24405400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:24402000-24403000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:24402200-24403000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:24402400-24403000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:24402400-24403000	Flanking Active TSS	Fetal Lung	lung
9	chr6:24402400-24403200	Active TSS	Brain Germinal Matrix	brain
10	chr6:24402400-24403200	Flanking Active TSS	Dnd41	blood
11	chr6:24402400-24406600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr6:24402600-24403000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:24402600-24403000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:24402600-24403000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr6:24402600-24403000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:24402600-24403000	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr6:24402600-24403000	Flanking Active TSS	Fetal Brain Male	brain
18	chr6:24402600-24403000	Flanking Active TSS	Fetal Kidney	kidney
19	chr6:24402600-24403200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:24402600-24403200	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr6:24402600-24403400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr6:24402600-24403800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:24402600-24403800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:24402600-24404000	Active TSS	Brain Angular Gyrus	brain
25	chr6:24402600-24404000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr6:24402600-24404000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:24402600-24404200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:24402600-24404200	Active TSS	Brain Substantia Nigra	brain
29	chr6:24402600-24404200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr6:24402600-24404400	Active TSS	Brain Cingulate Gyrus	brain
31	chr6:24402600-24404400	Active TSS	A549	lung
32	chr6:24402600-24404600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr6:24402600-24404600	Active TSS	Rectal Smooth Muscle	rectum
34	chr6:24402600-24404600	Active TSS	Stomach Smooth Muscle	stomach
35	chr6:24402600-24404800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:24402600-24405000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr6:24402600-24405200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:24402600-24405400	Active TSS	H9 Cell Line	embryonic stem cell
39	chr6:24402600-24405600	Active TSS	GM12878-XiMat	blood
40	chr6:24402800-24403000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr6:24402800-24403000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr6:24402800-24403000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:24402800-24403000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr6:24402800-24403000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:24402800-24403000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr6:24402800-24403000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:24402800-24403000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr6:24402800-24403000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr6:24402800-24403000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:24402800-24403000	Active TSS	Aorta	Aorta

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