Variant report

Variant	rs17417084
Chromosome Location	chr7:39706650-39706651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39705505..39707124-chr7:39714403..39716218,2	K562	blood:
2	chr7:39706072..39707663-chr7:39987856..39989855,2	K562	blood:
3	chr7:39696448..39698562-chr7:39706313..39708864,2	K562	blood:

Variant related genes	Relation type
ENSG00000259826	Chromatin interaction
ENSG00000065883	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10253933	0.83[ASN][1000 genomes]
rs10267545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10486803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11773499	1.00[JPT][hapmap]
rs12668144	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12669963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12701754	0.96[ASN][1000 genomes]
rs12701755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701756	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12701757	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13247563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17417049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34063025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35774126	1.00[ASN][1000 genomes]
rs35943406	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3779200	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6462940	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968684	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976944	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];1.00[ASN][1000 genomes]
rs6977082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7778955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7779169	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7792940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9648483	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:87 , 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	chr7:39691800-39707000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr7:39691800-39708800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr7:39692000-39707000	Weak transcription	Stomach Mucosa	stomach
12	chr7:39692000-39707000	Weak transcription	HSMMtube	muscle
13	chr7:39692000-39707200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr7:39692200-39714000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:39697600-39707000	Weak transcription	Adipose Nuclei	Adipose
16	chr7:39697800-39707000	Weak transcription	HSMM	muscle
17	chr7:39698800-39707000	Weak transcription	Left Ventricle	heart
18	chr7:39699400-39707000	Weak transcription	Ovary	ovary
19	chr7:39699400-39712000	Weak transcription	Fetal Kidney	kidney
20	chr7:39699600-39707000	Weak transcription	Osteobl	bone
21	chr7:39700000-39707000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:39700000-39728200	Weak transcription	Liver	Liver
23	chr7:39701200-39718400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr7:39701800-39708200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:39701800-39716400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:39701800-39720800	Weak transcription	Lung	lung
27	chr7:39701800-39721200	Weak transcription	Thymus	Thymus
28	chr7:39701800-39722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
30	chr7:39702000-39707000	Weak transcription	Right Ventricle	heart
31	chr7:39702000-39709200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:39702000-39716600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr7:39702000-39727400	Weak transcription	Fetal Intestine Large	intestine
34	chr7:39702200-39716400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr7:39702600-39707000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:39702800-39706800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr7:39702800-39707000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr7:39703200-39707000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:39703800-39711800	Weak transcription	GM12878-XiMat	blood
40	chr7:39703800-39716600	Weak transcription	Fetal Muscle Leg	muscle
41	chr7:39704000-39708000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr7:39704000-39714600	Weak transcription	Primary T cells from cord blood	blood
43	chr7:39704200-39716400	Weak transcription	Fetal Intestine Small	intestine
44	chr7:39704200-39716600	Weak transcription	Psoas Muscle	Psoas
45	chr7:39704400-39708400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:39704400-39711000	Weak transcription	NHEK	skin
47	chr7:39704400-39714800	Weak transcription	Primary B cells from cord blood	blood
48	chr7:39704400-39716200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:39704400-39717800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr7:39704600-39707000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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