Variant report

Variant	rs4699639
Chromosome Location	chr4:99444032-99444033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99441293..99445376-chr4:99447706..99451023,3	K562	blood:
2	chr4:99443782..99445449-chr4:99579317..99581605,2	MCF-7	breast:
3	chr4:99413602..99415848-chr4:99442433..99444375,2	K562	blood:

Variant related genes	Relation type
ENSG00000168785	Chromatin interaction
ENSG00000260641	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10002696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10004753	0.81[CHB][hapmap]
rs10005781	0.81[CHB][hapmap]
rs10006366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10006430	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10018825	0.92[CEU][hapmap];0.90[CHB][hapmap]
rs10021296	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs10025051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097619	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13108940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116201	0.81[CHB][hapmap]
rs13123700	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141997	0.88[CEU][hapmap]
rs13149070	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs1528547	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1534555	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1573478	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap]
rs1919210	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1919211	0.81[CEU][hapmap]
rs2037832	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2866016	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs2866017	0.92[CEU][hapmap];0.90[CHB][hapmap]
rs28886705	0.84[ASN][1000 genomes]
rs4447870	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699344	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699345	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4699348	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4699349	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs4699353	0.81[JPT][hapmap]
rs4699354	0.94[JPT][hapmap]
rs4699640	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699644	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699646	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4699648	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6532742	0.92[CEU][hapmap]
rs6532751	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs6815038	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6823547	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6831643	0.92[CEU][hapmap]
rs6837359	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6847124	0.83[ASN][1000 genomes]
rs71600251	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7672134	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs7678323	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs9760870	0.86[ASN][1000 genomes]

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	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99436600-99446400	Weak transcription	Left Ventricle	heart
2	chr4:99438800-99452000	Enhancers	Fetal Heart	heart
3	chr4:99439600-99445800	Enhancers	Ovary	ovary
4	chr4:99440400-99458400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:99441200-99446400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr4:99441800-99446400	Weak transcription	Spleen	Spleen
7	chr4:99442200-99446000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr4:99442200-99446000	Enhancers	NHEK	skin
9	chr4:99442200-99450600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr4:99442400-99444600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:99442400-99444800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:99442400-99445800	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:99442400-99446600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:99442400-99446800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:99442600-99444400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:99442600-99444800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:99442600-99445200	Enhancers	HMEC	breast
18	chr4:99442600-99445400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:99442600-99445400	Enhancers	HSMM	muscle
20	chr4:99442600-99445600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr4:99442600-99445600	Enhancers	Brain Substantia Nigra	brain
22	chr4:99442600-99445600	Enhancers	NHLF	lung
23	chr4:99442600-99445800	Enhancers	Rectal Smooth Muscle	rectum
24	chr4:99442600-99446000	Enhancers	Brain Angular Gyrus	brain
25	chr4:99442600-99446000	Enhancers	Brain Germinal Matrix	brain
26	chr4:99442600-99446000	Enhancers	Fetal Lung	lung
27	chr4:99442600-99446000	Enhancers	Fetal Stomach	stomach
28	chr4:99442600-99446600	Enhancers	Brain Hippocampus Middle	brain
29	chr4:99442600-99446800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:99442600-99447400	Enhancers	Brain Anterior Caudate	brain
31	chr4:99442800-99444200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr4:99442800-99444400	Enhancers	HSMMtube	muscle
33	chr4:99442800-99445800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:99442800-99445800	Enhancers	A549	lung
35	chr4:99443000-99446800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:99443200-99444200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:99443200-99444400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr4:99443200-99444600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:99443200-99444600	Flanking Active TSS	NH-A	brain
40	chr4:99443200-99445200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr4:99443400-99444200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr4:99443400-99444400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:99443400-99444400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr4:99443400-99444400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:99443400-99444600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:99443400-99444600	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:99443600-99444200	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr4:99443600-99444400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:99443600-99444400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:99443600-99444400	Flanking Active TSS	HUVEC	blood vessel

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