Variant report

Variant	rs7895872
Chromosome Location	chr10:112678657-112678658
allele	G/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	YY1	chr10:112678161-112679755	ECC-1	luminal epithelium:	n/a	chr10:112678465-112678474
2	TAF1	chr10:112678116-112679167	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr10:112677940-112679208	U87	brain:	n/a	n/a
4	MAX	chr10:112678133-112679130	A549	lung:	n/a	n/a
5	SRF	chr10:112678451-112678835	GM12878	blood:	n/a	chr10:112678676-112678694
6	RCOR1	chr10:112678156-112679588	K562	blood:	n/a	n/a
7	EGR1	chr10:112678270-112679217	H1-hESC	embryonic stem cell:	n/a	chr10:112678304-112678317 chr10:112678304-112678317 chr10:112678300-112678322 chr10:112678304-112678318 chr10:112678305-112678316 chr10:112678456-112678465 chr10:112678306-112678316
8	YY1	chr10:112678267-112679171	GM12892	blood:	n/a	chr10:112678465-112678474
9	GABPA	chr10:112678108-112679344	A549	lung:	n/a	n/a
10	HEY1	chr10:112678236-112679059	K562	blood:	n/a	n/a
11	IRF1	chr10:112678081-112679202	K562	blood:	n/a	chr10:112678359-112678373 chr10:112679118-112679127
12	REST	chr10:112678281-112678812	K562	blood:	n/a	chr10:112678469-112678482
13	POLR2A	chr10:112677286-112679707	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr10:112678059-112679712	Hela-S3	cervix:	n/a	n/a
15	SIN3AK20	chr10:112678638-112679069	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr10:112678209-112679240	GM12878	blood:	n/a	n/a
17	TAF1	chr10:112678037-112679803	ECC-1	luminal epithelium:	n/a	n/a
18	CEBPB	chr10:112678213-112679549	Hela-S3	cervix:	n/a	n/a
19	PML	chr10:112678079-112679284	MCF-7	breast:	n/a	n/a
20	YY1	chr10:112678169-112679260	GM12878	blood:	n/a	chr10:112678465-112678474
21	GABPA	chr10:112678284-112679283	HepG2	liver:	n/a	n/a
22	RELA	chr10:112678080-112679554	GM10847	blood:	n/a	n/a
23	POU2F2	chr10:112677960-112679274	GM12878	blood:	n/a	n/a
24	EP300	chr10:112678299-112679199	HepG2	liver:	n/a	chr10:112678705-112678712
25	TAF1	chr10:112678163-112679192	Hela-S3	cervix:	n/a	n/a
26	MAX	chr10:112678119-112679626	NB4	blood:	n/a	n/a
27	TAF7	chr10:112678272-112678689	H1-hESC	embryonic stem cell:	n/a	n/a
28	JUND	chr10:112678235-112678686	A549	lung:	n/a	n/a
29	ELF1	chr10:112678178-112679653	MCF-7	breast:	n/a	chr10:112678705-112678714
30	POLR2A	chr10:112677941-112679250	PANC-1	pancreas:	n/a	n/a
31	SP1	chr10:112678147-112678726	GM12878	blood:	n/a	chr10:112678309-112678319 chr10:112678458-112678467 chr10:112678363-112678372 chr10:112678348-112678357 chr10:112678457-112678469 chr10:112678347-112678359 chr10:112678457-112678469 chr10:112678361-112678373 chr10:112678459-112678468
32	POLR2A	chr10:112678150-112679838	GM19099	blood:	n/a	n/a
33	YY1	chr10:112678134-112679653	HCT-116	colon:	n/a	chr10:112678465-112678474
34	POLR2A	chr10:112678051-112679648	HepG2	liver:	n/a	n/a
35	SIN3AK20	chr10:112677956-112680323	MCF-7	breast:	n/a	n/a
36	ATF1	chr10:112678460-112679251	K562	blood:	n/a	n/a
37	RELA	chr10:112677966-112679552	GM19099	blood:	n/a	n/a
38	RCOR1	chr10:112678384-112679187	K562	blood:	n/a	n/a
39	RCOR1	chr10:112678068-112679620	Hela-S3	cervix:	n/a	n/a
40	MYC	chr10:112678235-112679229	K562	blood:	n/a	n/a
41	POLR2A	chr10:112678173-112679733	H1-neurons	neurons:	n/a	n/a
42	ELF1	chr10:112678240-112679220	HepG2	liver:	n/a	chr10:112678705-112678714
43	SIN3A	chr10:112678025-112680453	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr10:112678219-112678721	A549	lung:	n/a	n/a
45	POLR2A	chr10:112677540-112680807	H1-hESC	embryonic stem cell:	n/a	n/a
46	SRF	chr10:112678153-112679288	MCF-7	breast:	n/a	chr10:112679249-112679259 chr10:112678209-112678227 chr10:112678676-112678694
47	HMGN3	chr10:112678223-112678712	K562	blood:	n/a	n/a
48	POLR2A	chr10:112678183-112679729	A549	lung:	n/a	n/a
49	EGR1	chr10:112678202-112678735	MCF-7	breast:	n/a	chr10:112678304-112678317 chr10:112678304-112678317 chr10:112678300-112678322 chr10:112678304-112678318 chr10:112678305-112678316 chr10:112678456-112678465 chr10:112678306-112678316
50	REST	chr10:112678386-112678678	SK-N-SH	brain:	n/a	chr10:112678469-112678482

No.	Distal block	Cell Line	Cell type
1	chr1:94311636..94312585-chr10:112678360..112678969,2	Hela-S3	cervix:
2	chr1:245027659..245028186-chr10:112678315..112679139,2	Hela-S3	cervix:
3	chr10:112654963..112658264-chr10:112677155..112680097,3	MCF-7	breast:
4	chr10:112678183..112678694-chr20:13694652..13695508,2	Hela-S3	cervix:
5	chr10:112675807..112678772-chr10:112678882..112681031,3	MCF-7	breast:
6	chr10:112630522..112633740-chr10:112677502..112680452,8	K562	blood:
7	chr10:112678311..112678962-chrX:100663187..100663738,2	Hela-S3	cervix:
8	chr10:112677828..112678683-chr16:777302..778639,3	Hela-S3	cervix:
9	chr10:112677742..112679922-chr10:112696330..112699215,3	K562	blood:
10	chr10:112664345..112669629-chr10:112675236..112680543,10	K562	blood:
11	chr10:112678657..112679724-chr17:48943326..48944208,3	Hela-S3	cervix:
12	chr10:112514937..112517303-chr10:112677339..112679296,2	K562	blood:
13	chr10:112678245..112678751-chr15:52860426..52861397,2	Hela-S3	cervix:
14	chr10:112678574..112679335-chr14:74416633..74417220,2	Hela-S3	cervix:
15	chr10:112678206..112678806-chr17:56756553..56757474,2	Hela-S3	cervix:
16	chr1:25664559..25665329-chr10:112678202..112679188,2	HCT-116	colon:
17	chr10:112404113..112406427-chr10:112678273..112680530,3	K562	blood:
18	chr10:112630838..112635784-chr10:112676837..112681433,10	K562	blood:
19	chr10:112678637..112679593-chr3:101405050..101405570,2	NB4	blood:
20	chr10:112677485..112680905-chr10:112696350..112700143,5	K562	blood:

Variant related genes	Relation type
SHOC2	TF binding region
ENSG00000183726	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000234118	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000265827	Chromatin interaction
ENSG00000114391	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000117616	Chromatin interaction
ENSG00000156050	Chromatin interaction
ENSG00000126945	Chromatin interaction
ENSG00000103253	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000150593	Chromatin interaction
ENSG00000214413	Chromatin interaction
ENSG00000203497	Chromatin interaction
ENSG00000252036	Chromatin interaction
ENSG00000108061	Chromatin interaction
ENSG00000273175	Chromatin interaction
ENSG00000203867	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000153187	Chromatin interaction
ENSG00000119723	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10787287	0.82[MKK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs10787289	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10787292	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs1322995	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1327548	0.84[EUR][1000 genomes]
rs1341051	0.83[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs1341053	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1359849	0.86[TSI][hapmap]
rs1410057	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs1581886	0.84[EUR][1000 genomes]
rs17128202	0.82[EUR][1000 genomes]
rs1927159	0.88[ASW][hapmap];0.81[MKK][hapmap]
rs4918607	0.83[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs553668	0.85[CHD][hapmap]
rs7067540	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7072816	0.81[EUR][1000 genomes]
rs7082572	0.85[EUR][1000 genomes]
rs7086350	0.91[TSI][hapmap]
rs7095404	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7101075	0.82[EUR][1000 genomes]
rs7899762	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7917192	0.82[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	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1051327	chr10:112650316-112772917	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540774	chr10:112650316-112772917	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1047865	chr10:112660427-112730573	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7895872	XPNPEP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112677400-112681000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr10:112677400-112681200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr10:112677400-112681200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:112677400-112684000	Active TSS	GM12878-XiMat	blood
5	chr10:112677600-112679000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr10:112677600-112680400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:112677600-112680400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr10:112677600-112680800	Active TSS	Aorta	Aorta
9	chr10:112677600-112680800	Active TSS	Psoas Muscle	Psoas
10	chr10:112677600-112681000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr10:112677600-112681000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr10:112677600-112681000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:112677600-112681000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:112677600-112681000	Active TSS	Colonic Mucosa	Colon
15	chr10:112677600-112681000	Active TSS	Fetal Stomach	stomach
16	chr10:112677600-112681000	Active TSS	Fetal Thymus	thymus
17	chr10:112677600-112681000	Active TSS	Right Atrium	heart
18	chr10:112677600-112681000	Active TSS	Right Ventricle	heart
19	chr10:112677600-112681200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr10:112677600-112682000	Active TSS	NHLF	lung
21	chr10:112677800-112680600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr10:112677800-112680600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr10:112677800-112680800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr10:112677800-112680800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr10:112677800-112680800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr10:112677800-112680800	Active TSS	Fetal Muscle Trunk	muscle
27	chr10:112677800-112680800	Active TSS	Fetal Muscle Leg	muscle
28	chr10:112677800-112680800	Active TSS	Placenta	Placenta
29	chr10:112677800-112680800	Active TSS	Ovary	ovary
30	chr10:112677800-112680800	Active TSS	HMEC	breast
31	chr10:112677800-112681000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr10:112677800-112681000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:112677800-112681000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:112677800-112681000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr10:112677800-112681000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:112677800-112681000	Active TSS	Fetal Intestine Large	intestine
37	chr10:112677800-112681000	Active TSS	Thymus	Thymus
38	chr10:112677800-112681400	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr10:112677800-112681400	Active TSS	A549	lung
40	chr10:112677800-112681600	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr10:112677800-112681600	Active TSS	K562	blood
42	chr10:112678000-112679000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
43	chr10:112678000-112679000	Active TSS	Fetal Heart	heart
44	chr10:112678000-112679200	Bivalent/Poised TSS	HepG2	liver
45	chr10:112678000-112679800	Active TSS	Brain Germinal Matrix	brain
46	chr10:112678000-112680000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr10:112678000-112680000	Active TSS	Brain Angular Gyrus	brain
48	chr10:112678000-112680000	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr10:112678000-112680200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:112678000-112680200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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