Variant report

Variant	rs1859480
Chromosome Location	chr7:39707834-39707835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39662103..39664147-chr7:39707477..39710458,2	MCF-7	breast:
2	chr7:39696448..39698562-chr7:39706313..39708864,2	K562	blood:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13228455	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17171612	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35569526	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4587238	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4723900	0.80[EUR][1000 genomes]
rs57164715	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61070404	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6462942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6967563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6969272	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6973745	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7805581	0.93[EUR][1000 genomes];0.98[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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39672200-39722800	Weak transcription	Hela-S3	cervix
2	chr7:39675200-39708800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:39680000-39721600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:39680800-39716400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:39682800-39722000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:39683400-39716600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr7:39683600-39712600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:39687400-39715000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr7:39691800-39708800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr7:39692200-39714000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:39699400-39712000	Weak transcription	Fetal Kidney	kidney
12	chr7:39700000-39728200	Weak transcription	Liver	Liver
13	chr7:39701200-39718400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr7:39701800-39708200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:39701800-39716400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr7:39701800-39720800	Weak transcription	Lung	lung
17	chr7:39701800-39721200	Weak transcription	Thymus	Thymus
18	chr7:39701800-39722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
20	chr7:39702000-39709200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:39702000-39716600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:39702000-39727400	Weak transcription	Fetal Intestine Large	intestine
23	chr7:39702200-39716400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:39703800-39711800	Weak transcription	GM12878-XiMat	blood
25	chr7:39703800-39716600	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:39704000-39708000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr7:39704000-39714600	Weak transcription	Primary T cells from cord blood	blood
28	chr7:39704200-39716400	Weak transcription	Fetal Intestine Small	intestine
29	chr7:39704200-39716600	Weak transcription	Psoas Muscle	Psoas
30	chr7:39704400-39708400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:39704400-39711000	Weak transcription	NHEK	skin
32	chr7:39704400-39714800	Weak transcription	Primary B cells from cord blood	blood
33	chr7:39704400-39716200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:39704400-39717800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr7:39704800-39714600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:39704800-39718600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr7:39705200-39716200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:39705800-39708200	Enhancers	NHDF-Ad	bronchial
39	chr7:39706000-39708000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:39706000-39708000	Strong transcription	HUVEC	blood vessel
41	chr7:39706400-39709600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:39706400-39710800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:39706400-39722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:39706600-39708000	Enhancers	Brain Angular Gyrus	brain
45	chr7:39706600-39716200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:39706800-39708000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr7:39707000-39708000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:39707000-39708000	Enhancers	Osteobl	bone
49	chr7:39707200-39710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr7:39707200-39711400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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