Variant report

Variant	rs4134903
Chromosome Location	chr7:99711040-99711041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99711026-99711150	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:99710730-99711317	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr7:99710984-99711300	HL-60	blood:	n/a	n/a
4	POLR2A	chr7:99710931-99711333	K562	blood:	n/a	n/a
5	POLR2A	chr7:99710912-99711203	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr7:99710960-99711117	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr7:99710778-99711342	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99709043..99711986-chr7:99718165..99719979,3	K562	blood:
2	chr7:99708863..99711392-chr7:99752836..99754442,2	K562	blood:
3	chr7:99709712..99711434-chr7:99720028..99722233,2	K562	blood:
4	chr7:99709639..99711480-chr7:99723026..99724757,2	K562	blood:

No data

Variant related genes	Relation type
TAF6	TF binding region
ENSG00000146826	Chromatin interaction
ENSG00000214309	Chromatin interaction
ENSG00000266154	Chromatin interaction
ENSG00000166997	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10228764	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10267212	0.84[MEX][hapmap]
rs10281368	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1060544	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1076237	0.84[MEX][hapmap]
rs11771139	0.84[ASW][hapmap];0.82[CEU][hapmap];0.98[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs11771331	0.85[MEX][hapmap]
rs12705070	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12705071	0.95[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs13223792	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13232115	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1527423	0.91[YRI][hapmap]
rs1534310	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1880949	0.84[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2070215	0.95[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2293479	0.95[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34031156	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35146811	0.84[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35991721	0.81[AFR][1000 genomes]
rs4424195	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4729566	0.85[MEX][hapmap]
rs4729576	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59261051	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6465760	0.84[MEX][hapmap]
rs6465761	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6465762	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6950205	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6953441	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6974305	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7788746	0.85[MEX][hapmap]
rs999885	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
9	nsv824235	chr7:99710452-99711111	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4134903	BUD31	cis	parietal	SCAN
rs4134903	GATS	cis	cerebellum	SCAN
rs4134903	ZSCAN21	cis	parietal	SCAN
rs4134903	PILRB	cis	parietal	SCAN
rs4134903	GATS	cis	parietal	SCAN
rs4134903	SERPINE1	cis	cerebellum	SCAN
rs4134903	GAL3ST4	cis	cerebellum	SCAN
rs4134903	ZKSCAN1	cis	cerebellum	SCAN
rs4134903	ZNF498	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99700200-99716200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:99700200-99716400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:99700400-99715800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:99700400-99716000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:99700400-99716200	Weak transcription	Psoas Muscle	Psoas
6	chr7:99700400-99716200	Weak transcription	Small Intestine	intestine
7	chr7:99700600-99711400	Strong transcription	Placenta	Placenta
8	chr7:99700600-99712000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:99700600-99712000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:99700600-99712000	Strong transcription	Lung	lung
11	chr7:99700600-99712400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr7:99700600-99713000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:99700600-99713200	Strong transcription	Fetal Muscle Leg	muscle
14	chr7:99700600-99714600	Strong transcription	Fetal Intestine Small	intestine
15	chr7:99700600-99715200	Strong transcription	Fetal Stomach	stomach
16	chr7:99700600-99716200	Weak transcription	Fetal Brain Male	brain
17	chr7:99700800-99711800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:99700800-99711800	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr7:99700800-99712000	Strong transcription	Brain Cingulate Gyrus	brain
20	chr7:99700800-99712000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr7:99700800-99712200	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:99700800-99712200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:99700800-99712600	Strong transcription	Colonic Mucosa	Colon
24	chr7:99700800-99713000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr7:99700800-99713000	Strong transcription	Thymus	Thymus
26	chr7:99700800-99714400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:99701000-99711600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:99701000-99711800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:99701000-99712000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr7:99701000-99712000	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr7:99701000-99712000	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:99701000-99712800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr7:99701000-99712800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:99701000-99712800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr7:99701000-99713000	Strong transcription	Fetal Thymus	thymus
36	chr7:99701000-99713000	Strong transcription	Spleen	Spleen
37	chr7:99701000-99713200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:99701000-99714000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr7:99701000-99714600	Strong transcription	Fetal Intestine Large	intestine
40	chr7:99701200-99711400	Strong transcription	Pancreas	Pancrea
41	chr7:99701200-99712000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr7:99701200-99712000	Strong transcription	Brain Germinal Matrix	brain
43	chr7:99701200-99712000	Strong transcription	Fetal Brain Female	brain
44	chr7:99701200-99712000	Strong transcription	Gastric	stomach
45	chr7:99701200-99712000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr7:99701200-99712000	Strong transcription	Dnd41	blood
47	chr7:99701200-99712200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:99701200-99712800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr7:99701200-99713000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:99701200-99714600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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