Variant report

Variant	rs6829297
Chromosome Location	chr4:99571085-99571086
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	chr4:99566031..99568525-chr4:99568795..99571513,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10001533	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10489126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10516435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027883	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17027886	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41399047	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831674	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7685150	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7699492	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs883510	1.00[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	nsv594940	chr4:99542475-99573350	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99548000-99577000	Weak transcription	Esophagus	oesophagus
2	chr4:99564000-99571600	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr4:99564400-99575600	Weak transcription	Fetal Kidney	kidney
4	chr4:99565200-99571200	Weak transcription	A549	lung
5	chr4:99565200-99571200	Weak transcription	NHEK	skin
6	chr4:99565200-99571400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:99565200-99571400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:99565200-99571400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:99565800-99571200	Enhancers	Brain Anterior Caudate	brain
10	chr4:99565800-99571200	Enhancers	Brain Substantia Nigra	brain
11	chr4:99566000-99571200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:99566000-99575200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:99567600-99574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:99567600-99574400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:99567600-99574800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:99568200-99571600	Enhancers	Fetal Brain Female	brain
17	chr4:99568200-99571600	Enhancers	NHDF-Ad	bronchial
18	chr4:99568400-99575000	Weak transcription	Thymus	Thymus
19	chr4:99569200-99571200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:99569200-99571200	Enhancers	Ovary	ovary
21	chr4:99569600-99578200	Weak transcription	Aorta	Aorta
22	chr4:99569600-99578400	Weak transcription	Spleen	Spleen
23	chr4:99569800-99571600	Enhancers	Brain Cingulate Gyrus	brain
24	chr4:99570000-99576800	Weak transcription	Fetal Stomach	stomach
25	chr4:99570200-99571600	Enhancers	Osteobl	bone
26	chr4:99570200-99571800	Weak transcription	HMEC	breast
27	chr4:99570200-99573800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:99570200-99573800	Weak transcription	Fetal Brain Male	brain
29	chr4:99570200-99577000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:99570200-99577000	Weak transcription	Fetal Heart	heart
31	chr4:99570400-99571400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:99570400-99573800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:99570600-99571200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:99570600-99572000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:99570600-99572200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:99570600-99573800	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:99570800-99571200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:99570800-99571200	Strong transcription	HSMM	muscle
39	chr4:99570800-99571400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:99570800-99571600	ZNF genes & repeats	NHLF	lung
41	chr4:99571000-99571200	Weak transcription	HUVEC	blood vessel
42	chr4:99571000-99571400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:99571000-99571800	Enhancers	Brain Angular Gyrus	brain
44	chr4:99571000-99573600	Weak transcription	NH-A	brain
45	chr4:99571000-99574200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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