Variant report

Variant	rs4690893
Chromosome Location	chr4:159083696-159083697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr4:159082522-159083724	HUVEC	blood vessel:	n/a	chr4:159082919-159082928 chr4:159082619-159082629
2	POLR2A	chr4:159082407-159084188	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr4:159082455-159084205	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:158918095..158920642-chr4:159082633..159084601,2	MCF-7	breast:
2	chr4:159011423..159013282-chr4:159081920..159084638,2	MCF-7	breast:
3	chr4:159075615..159078408-chr4:159081390..159084163,2	MCF-7	breast:
4	chr4:159075926..159078246-chr4:159082036..159083759,2	K562	blood:
5	chr4:159041667..159043431-chr4:159082269..159084157,2	MCF-7	breast:
6	chr4:159013562..159016824-chr4:159081048..159085392,5	MCF-7	breast:
7	chr4:159083602..159085343-chr4:159091716..159093896,2	K562	blood:

No data

Variant related genes	Relation type
FAM198B	TF binding region
ENSG00000164125	Chromatin interaction
ENSG00000248429	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10005007	1.00[ASN][1000 genomes]
rs10007737	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008208	1.00[JPT][hapmap]
rs10012339	1.00[JPT][hapmap]
rs10016822	0.84[EUR][1000 genomes]
rs10018872	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10024133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10026876	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028490	1.00[JPT][hapmap]
rs10517689	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100150	1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937022	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11938464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12502811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645131	1.00[JPT][hapmap]
rs12648410	1.00[JPT][hapmap]
rs13113959	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1320370	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1320371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs14202	1.00[JPT][hapmap]
rs17036927	1.00[CEU][hapmap]
rs2346319	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346321	1.00[JPT][hapmap]
rs2346381	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346774	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28499342	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28691778	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28719822	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881373	1.00[JPT][hapmap]
rs2881473	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234917	1.00[JPT][hapmap]
rs4317248	1.00[JPT][hapmap]
rs4324593	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4345228	1.00[JPT][hapmap]
rs4391084	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501266	1.00[JPT][hapmap]
rs4582199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4627913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691455	1.00[JPT][hapmap]
rs4691456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691459	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691461	1.00[JPT][hapmap]
rs4691462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6536299	1.00[JPT][hapmap]
rs6812635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6813306	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819576	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820988	1.00[JPT][hapmap]
rs6821598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6830702	1.00[JPT][hapmap]
rs6832099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833198	1.00[JPT][hapmap]
rs6834164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849902	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6852646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6855420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671094	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686997	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8370	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159072000-159083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:159076600-159085200	Enhancers	Colon Smooth Muscle	Colon
3	chr4:159076800-159089800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:159078400-159089000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:159078600-159094000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:159079200-159084000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:159079400-159084000	Enhancers	NH-A	brain
8	chr4:159079800-159084000	Genic enhancers	HSMM	muscle
9	chr4:159080400-159084000	Enhancers	Brain Anterior Caudate	brain
10	chr4:159080600-159085200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:159080600-159086000	Weak transcription	Fetal Intestine Large	intestine
12	chr4:159080800-159085800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:159080800-159085800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:159081200-159083800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:159081400-159085000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:159081600-159084000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:159081600-159085400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:159081800-159084000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:159082000-159084000	Enhancers	Brain Substantia Nigra	brain
20	chr4:159082000-159085400	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:159082600-159083800	Enhancers	Fetal Stomach	stomach
22	chr4:159082600-159083800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr4:159082600-159084000	Enhancers	A549	lung
24	chr4:159082600-159084200	Genic enhancers	HepG2	liver
25	chr4:159082600-159084200	Enhancers	NHLF	lung
26	chr4:159082600-159084200	Enhancers	Osteobl	bone
27	chr4:159082800-159083800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr4:159082800-159084200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:159083000-159083800	Flanking Active TSS	HUVEC	blood vessel
30	chr4:159083000-159084000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr4:159083000-159084200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:159083000-159084400	Enhancers	Right Ventricle	heart
33	chr4:159083000-159086000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:159083000-159086000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr4:159083000-159086800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr4:159083000-159091800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:159083200-159083800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:159083200-159083800	Enhancers	Rectal Smooth Muscle	rectum
39	chr4:159083200-159084000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:159083200-159084200	Enhancers	Adipose Nuclei	Adipose
41	chr4:159083200-159084400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:159083200-159085800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:159083200-159085800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:159083200-159085800	Weak transcription	Psoas Muscle	Psoas
45	chr4:159083200-159087200	Weak transcription	Fetal Intestine Small	intestine
46	chr4:159083200-159089800	Weak transcription	Fetal Kidney	kidney
47	chr4:159083400-159083800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:159083400-159084200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:159083400-159085000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:159083400-159085000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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