Variant report

Variant	rs10516434
Chromosome Location	chr4:99445315-99445316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000260641	Chromatin interaction
ENSG00000168785	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10004753	0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs10489125	0.82[JPT][hapmap]
rs10516433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945713	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116201	0.94[YRI][hapmap];0.80[AFR][1000 genomes]
rs1554849	0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17498778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17499015	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17564872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17564998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699642	0.92[YRI][hapmap]
rs4699645	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699654	0.82[JPT][hapmap]
rs56221164	1.00[ASN][1000 genomes]
rs59150136	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60026821	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60947018	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6532740	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];0.98[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532746	0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6817773	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6830136	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840239	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6840610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6846101	0.90[ASN][1000 genomes]
rs6853079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666585	0.82[JPT][hapmap]
rs7667273	0.82[JPT][hapmap]
rs7667608	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676155	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688849	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689116	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9761395	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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:55 , 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	chr4:99442400-99445800	Enhancers	Brain Cingulate Gyrus	brain
11	chr4:99442400-99446600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:99442400-99446800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:99442600-99445400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:99442600-99445400	Enhancers	HSMM	muscle
15	chr4:99442600-99445600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr4:99442600-99445600	Enhancers	Brain Substantia Nigra	brain
17	chr4:99442600-99445600	Enhancers	NHLF	lung
18	chr4:99442600-99445800	Enhancers	Rectal Smooth Muscle	rectum
19	chr4:99442600-99446000	Enhancers	Brain Angular Gyrus	brain
20	chr4:99442600-99446000	Enhancers	Brain Germinal Matrix	brain
21	chr4:99442600-99446000	Enhancers	Fetal Lung	lung
22	chr4:99442600-99446000	Enhancers	Fetal Stomach	stomach
23	chr4:99442600-99446600	Enhancers	Brain Hippocampus Middle	brain
24	chr4:99442600-99446800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:99442600-99447400	Enhancers	Brain Anterior Caudate	brain
26	chr4:99442800-99445800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:99442800-99445800	Enhancers	A549	lung
28	chr4:99443000-99446800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:99443600-99445800	Enhancers	Fetal Brain Male	brain
30	chr4:99443800-99445800	Enhancers	Fetal Brain Female	brain
31	chr4:99444000-99446000	Enhancers	Colon Smooth Muscle	Colon
32	chr4:99444400-99445800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:99444400-99446000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:99444400-99446600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:99444400-99446600	Enhancers	HUVEC	blood vessel
36	chr4:99444400-99446600	Enhancers	Osteobl	bone
37	chr4:99444400-99448800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:99444600-99445800	Enhancers	Fetal Muscle Leg	muscle
39	chr4:99444600-99446000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:99444600-99446600	Enhancers	NH-A	brain
41	chr4:99444600-99446800	Enhancers	NHDF-Ad	bronchial
42	chr4:99444600-99447200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr4:99444600-99450200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:99444800-99446800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:99444800-99447200	Weak transcription	Fetal Intestine Small	intestine
46	chr4:99444800-99448600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:99445000-99445800	Enhancers	Stomach Mucosa	stomach
48	chr4:99445000-99446400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:99445200-99445400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:99445200-99445600	Enhancers	Brain Inferior Temporal Lobe	brain

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