Variant report

Variant	rs4699196
Chromosome Location	chr4:106630949-106630950
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	CTCF	chr4:106630900-106631050	HepG2	liver:	n/a	n/a
2	E2F4	chr4:106629501-106631151	MCF10A-Er-Src	breast:	n/a	chr4:106630312-106630324 chr4:106630650-106630661 chr4:106630650-106630661
3	POLR2A	chr4:106630788-106631103	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr4:106628559-106631071	SK-N-SH	brain:	n/a	n/a
5	CUX1	chr4:106630844-106630966	K562	blood:	n/a	n/a
6	POLR2A	chr4:106630791-106632708	K562	blood:	n/a	n/a
7	RFX5	chr4:106628987-106632419	SK-N-SH	brain:	n/a	chr4:106629352-106629361 chr4:106630732-106630749 chr4:106631958-106631972 chr4:106631963-106631971 chr4:106631960-106631969 chr4:106631957-106631972
8	POLR2A	chr4:106628754-106631181	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:106394755..106397717-chr4:106629970..106632343,2	MCF-7	breast:
2	chr4:106628392..106631014-chr4:106816298..106818181,3	MCF-7	breast:
3	chr4:106628549..106631300-chr4:106636039..106639035,3	MCF-7	breast:
4	chr4:106393199..106396342-chr4:106628328..106631625,4	K562	blood:
5	chr4:106619847..106624541-chr4:106627186..106631133,7	MCF-7	breast:
6	chr4:106614729..106617409-chr4:106629462..106630998,2	MCF-7	breast:
7	chr4:106393678..106396634-chr4:106628055..106631625,3	K562	blood:
8	chr4:106616699..106623307-chr4:106623731..106631342,11	K562	blood:
9	chr4:106628554..106633489-chr4:106634205..106639726,8	K562	blood:

Variant related genes	Relation type
INTS12	TF binding region
GSTCD	TF binding region
ENSG00000138780	Chromatin interaction
ENSG00000168743	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000138777	Chromatin interaction
ENSG00000236699	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10025790	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs10516523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722731	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11933386	0.81[EUR][1000 genomes]
rs11933466	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[TSI][hapmap]
rs11934139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11941690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12639750	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1294667	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1294669	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1294670	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1294673	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13120110	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13138544	0.85[CHD][hapmap]
rs13147012	0.85[ASN][1000 genomes]
rs13148869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17036098	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17262764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044536	0.82[CEU][hapmap];0.95[CHD][hapmap]
rs2080789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2544395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2544398	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs2544404	0.81[EUR][1000 genomes]
rs2544405	0.81[EUR][1000 genomes]
rs2544406	0.82[CHB][hapmap]
rs2544408	0.82[CHB][hapmap]
rs2544409	0.82[CHB][hapmap]
rs2544412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2544413	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2544425	0.82[CHB][hapmap]
rs2553432	0.81[EUR][1000 genomes]
rs2553436	0.81[EUR][1000 genomes]
rs2553438	0.80[EUR][1000 genomes]
rs2553441	0.81[EUR][1000 genomes]
rs2553449	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2553453	0.82[CHB][hapmap]
rs2553458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553462	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28628106	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756260	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6820200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680134	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7684442	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7684839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7685231	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][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	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106628400-106631000	Active TSS	Psoas Muscle	Psoas
2	chr4:106628600-106631000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:106628600-106631800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:106628800-106631000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:106628800-106631000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:106628800-106631000	Active TSS	Fetal Intestine Large	intestine
7	chr4:106628800-106631000	Active TSS	Fetal Muscle Leg	muscle
8	chr4:106628800-106631000	Active TSS	Fetal Thymus	thymus
9	chr4:106628800-106631000	Active TSS	Right Ventricle	heart
10	chr4:106628800-106631400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr4:106628800-106631400	Active TSS	A549	lung
12	chr4:106628800-106631600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:106628800-106631800	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr4:106628800-106631800	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr4:106629000-106631000	Active TSS	Fetal Intestine Small	intestine
16	chr4:106629000-106631000	Active TSS	Fetal Kidney	kidney
17	chr4:106629000-106631000	Active TSS	Hela-S3	cervix
18	chr4:106629000-106631400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:106629000-106631400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr4:106629000-106631400	Active TSS	NHLF	lung
21	chr4:106629000-106631800	Active TSS	HMEC	breast
22	chr4:106629000-106632200	Active TSS	K562	blood
23	chr4:106629200-106631000	Active TSS	Fetal Stomach	stomach
24	chr4:106629200-106631000	Active TSS	NHEK	skin
25	chr4:106629200-106631200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:106629200-106631200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:106629200-106631200	Active TSS	NHDF-Ad	bronchial
28	chr4:106630200-106631000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr4:106630200-106631000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr4:106630200-106631000	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr4:106630200-106631000	Flanking Active TSS	Liver	Liver
32	chr4:106630400-106631000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:106630400-106631000	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr4:106630400-106631000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr4:106630400-106631000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr4:106630400-106631000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:106630400-106631000	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr4:106630400-106631000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:106630400-106631000	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr4:106630400-106631000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr4:106630400-106631000	Flanking Active TSS	Fetal Brain Male	brain
42	chr4:106630400-106631000	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr4:106630400-106631000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr4:106630400-106631000	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr4:106630400-106631000	Flanking Active TSS	Osteobl	bone
46	chr4:106630400-106631200	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr4:106630400-106631200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr4:106630400-106631200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:106630400-106631200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:106630400-106631200	Flanking Active TSS	Fetal Lung	lung

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