Variant report

Variant	rs17027628
Chromosome Location	chr4:99428608-99428609
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99422257..99425679-chr4:99427577..99430821,3	MCF-7	breast:
2	chr4:99424011..99426189-chr4:99427302..99429142,2	K562	blood:
3	chr4:99428008..99431537-chr4:99432874..99435399,3	MCF-7	breast:
4	chr4:99427354..99429199-chr4:99578326..99579998,2	MCF-7	breast:
5	chr4:99422565..99426189-chr4:99427302..99431103,4	K562	blood:

Variant related genes	Relation type
ENSG00000168785	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2091547	0.82[JPT][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs2866018	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4282188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4399995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4535338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61610951	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72893012	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7668981	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs7671986	0.87[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs955931	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99396200-99431400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:99397600-99439400	Weak transcription	Primary B cells from cord blood	blood
3	chr4:99400000-99429800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:99405600-99431000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:99408000-99432200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr4:99409800-99431600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:99413800-99430200	Weak transcription	HMEC	breast
8	chr4:99416200-99431600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:99416600-99430800	Weak transcription	Thymus	Thymus
10	chr4:99416800-99429600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:99417200-99431200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:99417600-99429800	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:99417600-99430200	Weak transcription	Brain Germinal Matrix	brain
14	chr4:99417800-99430600	Weak transcription	Fetal Kidney	kidney
15	chr4:99417800-99438600	Weak transcription	Right Atrium	heart
16	chr4:99418000-99430000	Weak transcription	Brain Anterior Caudate	brain
17	chr4:99419600-99436400	Weak transcription	HUVEC	blood vessel
18	chr4:99420200-99430200	Weak transcription	Fetal Brain Female	brain
19	chr4:99420200-99435800	Weak transcription	Spleen	Spleen
20	chr4:99420400-99430200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:99420400-99430200	Weak transcription	Brain Substantia Nigra	brain
22	chr4:99420400-99430400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:99420400-99431000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:99420400-99436400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:99420400-99436400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:99420600-99430000	Weak transcription	Brain Angular Gyrus	brain
27	chr4:99420600-99430200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:99420600-99430600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:99423000-99434200	Weak transcription	Aorta	Aorta
30	chr4:99423000-99434200	Weak transcription	Esophagus	oesophagus
31	chr4:99423600-99430200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr4:99423800-99431000	Weak transcription	NHEK	skin
33	chr4:99424400-99430200	Weak transcription	HSMM	muscle
34	chr4:99424600-99431000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:99424800-99430800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:99424800-99431200	Weak transcription	Primary T cells from cord blood	blood
37	chr4:99425000-99436200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:99425400-99429400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr4:99425600-99434200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:99425800-99431000	Weak transcription	Fetal Thymus	thymus
41	chr4:99426200-99429200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:99426600-99430200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:99426800-99430000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:99427000-99430200	Weak transcription	Osteobl	bone
45	chr4:99427000-99430400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:99427000-99430400	Weak transcription	Fetal Stomach	stomach
47	chr4:99427200-99429200	Weak transcription	Ovary	ovary
48	chr4:99427400-99429200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:99427600-99429800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:99427800-99429000	Strong transcription	NHDF-Ad	bronchial

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