Variant report

Variant	rs6718647
Chromosome Location	chr2:37310852-37310853
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	SIN3AK20	chr2:37310721-37312125	MCF-7	breast:	n/a	n/a
2	MAX	chr2:37310787-37312103	HepG2	liver:	n/a	n/a
3	MXI1	chr2:37310017-37312964	SK-N-SH	brain:	n/a	n/a
4	RUNX3	chr2:37310825-37312188	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:37310844-37311947	K562	blood:	n/a	n/a
6	SIN3A	chr2:37310818-37311975	GM12878	blood:	n/a	n/a
7	MXI1	chr2:37310844-37312218	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:37310832-37312049	Hela-S3	cervix:	n/a	n/a
9	MAX	chr2:37310795-37312070	MCF-7	breast:	n/a	n/a
10	TCF12	chr2:37310816-37312066	A549	lung:	n/a	n/a
11	MXI1	chr2:37310683-37312604	IMR90	lung:	n/a	n/a
12	MYBL2	chr2:37310826-37311827	HepG2	liver:	n/a	n/a
13	ZEB1	chr2:37310792-37311959	GM12878	blood:	n/a	chr2:37310995-37311006
14	MYC	chr2:37310769-37311644	H1-hESC	embryonic stem cell:	n/a	chr2:37310783-37310792
15	RFX5	chr2:37310805-37312025	Hela-S3	cervix:	n/a	n/a
16	HA-E2F1	chr2:37310801-37311991	MCF-7	breast:	n/a	chr2:37311544-37311553 chr2:37311520-37311529 chr2:37311657-37311666
17	MAX	chr2:37310840-37311997	ECC-1	luminal epithelium:	n/a	n/a
18	SIN3AK20	chr2:37310848-37311989	K562	blood:	n/a	n/a
19	POLR2A	chr2:37310764-37311938	MCF10A-Er-Src	breast:	n/a	n/a
20	PML	chr2:37310826-37312195	GM12878	blood:	n/a	n/a
21	MYC	chr2:37310842-37312152	K562	blood:	n/a	n/a
22	MAX	chr2:37310828-37312020	A549	lung:	n/a	n/a
23	ELF1	chr2:37310840-37311910	GM12878	blood:	n/a	n/a
24	REST	chr2:37310757-37312299	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr2:37310802-37311972	Hela-S3	cervix:	n/a	n/a
26	MAX	chr2:37310830-37311993	K562	blood:	n/a	n/a
27	E2F6	chr2:37310812-37311708	H1-hESC	embryonic stem cell:	n/a	chr2:37311544-37311553 chr2:37311520-37311529 chr2:37311657-37311666
28	TCF7L2	chr2:37310814-37311192	PANC-1	pancreas:	n/a	n/a
29	STAT3	chr2:37310806-37311006	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr2:37310815-37312024	GM12892	blood:	n/a	n/a
31	SIN3AK20	chr2:37310847-37312041	SK-N-SH	brain:	n/a	n/a
32	HCFC1	chr2:37310592-37312256	Hela-S3	cervix:	n/a	n/a
33	TEAD4	chr2:37310843-37312174	K562	blood:	n/a	n/a
34	MAX	chr2:37310796-37312078	SK-N-SH	brain:	n/a	n/a
35	CHD1	chr2:37310791-37311552	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:37310526-37312261	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr2:37310803-37311943	GM12892	blood:	n/a	n/a
38	MAX	chr2:37310744-37311995	ECC-1	luminal epithelium:	n/a	chr2:37310783-37310792
39	MYBL2	chr2:37310726-37312055	HepG2	liver:	n/a	n/a
40	MAX	chr2:37310750-37312237	A549	lung:	n/a	chr2:37310783-37310792
41	ZNF143	chr2:37310834-37311894	GM12878	blood:	n/a	chr2:37311478-37311496 chr2:37311565-37311583
42	MAX	chr2:37310808-37311744	MCF-7	breast:	n/a	n/a
43	TCF7L2	chr2:37310836-37311909	Hela-S3	cervix:	n/a	n/a
44	SIN3AK20	chr2:37310846-37311983	HepG2	liver:	n/a	n/a
45	SIN3A	chr2:37310787-37312290	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr2:37310793-37312004	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:37192443..37195662-chr2:37309226..37313144,4	K562	blood:
2	chr2:37303145..37307773-chr2:37309967..37312516,4	MCF-7	breast:
3	chr2:37310057..37313374-chr2:37313742..37317078,6	K562	blood:

Variant related genes	Relation type
GPATCH11	TF binding region
ENSG00000115808	Chromatin interaction
ENSG00000152133	Chromatin interaction
ENSG00000008869	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10176233	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs10176303	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10188586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10191403	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10194972	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12465097	0.97[AFR][1000 genomes]
rs12469391	0.97[AFR][1000 genomes]
rs13398187	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs13425846	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17020185	0.80[YRI][hapmap]
rs2307483	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs2373114	0.87[CEU][hapmap]
rs2541001	0.95[EUR][1000 genomes]
rs3845782	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs4648202	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs6732075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7596489	1.00[CEU][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6718647	CCDC75	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37308800-37313200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:37309600-37311000	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr2:37309600-37311000	Flanking Active TSS	Dnd41	blood
4	chr2:37310000-37311000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr2:37310000-37311200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:37310000-37311400	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr2:37310200-37311000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:37310200-37311000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:37310200-37311000	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr2:37310200-37311000	Flanking Active TSS	Fetal Brain Male	brain
11	chr2:37310200-37311000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr2:37310200-37311000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr2:37310200-37311000	Flanking Active TSS	Hela-S3	cervix
14	chr2:37310200-37311000	Flanking Active TSS	HUVEC	blood vessel
15	chr2:37310200-37311200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr2:37310200-37311200	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr2:37310200-37312400	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr2:37310200-37313000	Active TSS	Right Atrium	heart
19	chr2:37310400-37311000	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr2:37310400-37311000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr2:37310400-37311000	Flanking Active TSS	NH-A	brain
22	chr2:37310400-37312000	Active TSS	Brain Cingulate Gyrus	brain
23	chr2:37310400-37312000	Active TSS	Pancreas	Pancrea
24	chr2:37310400-37312200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:37310400-37312400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr2:37310400-37312400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:37310400-37312600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:37310400-37312600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr2:37310400-37312600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr2:37310400-37312600	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr2:37310400-37312600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:37310400-37312600	Active TSS	GM12878-XiMat	blood
33	chr2:37310600-37311000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr2:37310600-37311000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr2:37310600-37311000	Flanking Active TSS	Liver	Liver
36	chr2:37310600-37311000	Active TSS	Brain Germinal Matrix	brain
37	chr2:37310600-37311000	Flanking Active TSS	Thymus	Thymus
38	chr2:37310600-37311000	Weak transcription	Spleen	Spleen
39	chr2:37310600-37311800	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr2:37310600-37312000	Active TSS	H1 Cell Line	embryonic stem cell
41	chr2:37310600-37312000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:37310600-37312000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:37310600-37312000	Active TSS	Brain Angular Gyrus	brain
44	chr2:37310600-37312000	Active TSS	Brain Anterior Caudate	brain
45	chr2:37310600-37312000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:37310600-37312000	Active TSS	Fetal Heart	heart
47	chr2:37310600-37312000	Active TSS	Fetal Intestine Small	intestine
48	chr2:37310600-37312000	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr2:37310600-37312000	Active TSS	Stomach Smooth Muscle	stomach
50	chr2:37310600-37312000	Active TSS	HMEC	breast

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