Variant report

Variant	rs9890508
Chromosome Location	chr17:37941394-37941395
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37939870..37942689-chr17:37949107..37950989,2	MCF-7	breast:
2	chr17:37934439..37938793-chr17:37938988..37943375,4	K562	blood:
3	chr17:37819866..37822108-chr17:37939920..37942163,2	MCF-7	breast:
4	chr17:37937140..37939112-chr17:37941348..37943043,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161405	Chromatin interaction
ENSG00000173991	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13341681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13380812	1.00[AMR][1000 genomes]
rs28407584	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28409251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28432878	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28433533	0.87[AFR][1000 genomes]
rs28464000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28494476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28498893	1.00[AMR][1000 genomes]
rs28505218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28627663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28661251	1.00[AMR][1000 genomes]
rs28673180	1.00[AMR][1000 genomes]
rs28714172	1.00[AMR][1000 genomes]
rs28882824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61737968	1.00[AMR][1000 genomes]
rs62065168	1.00[AMR][1000 genomes]
rs9890819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9893628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9893933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9895237	1.00[AMR][1000 genomes]
rs9896961	1.00[AMR][1000 genomes]
rs9897451	1.00[AMR][1000 genomes]
rs9897847	1.00[AMR][1000 genomes]
rs9899977	1.00[AMR][1000 genomes]
rs9900885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9911163	1.00[AMR][1000 genomes]
rs9913746	1.00[AMR][1000 genomes]
rs9914556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9916301	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37938800-37942400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr17:37939000-37941600	Weak transcription	Fetal Thymus	thymus
3	chr17:37939000-37943200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr17:37939000-37944400	Weak transcription	Thymus	Thymus
5	chr17:37939000-37961800	Weak transcription	Spleen	Spleen
6	chr17:37939600-37943400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:37939800-37942400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:37939800-37943400	Weak transcription	NHEK	skin
9	chr17:37939800-37943800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:37939800-37944000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:37939800-37944000	Weak transcription	HMEC	breast
12	chr17:37940000-37948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr17:37940200-37943400	Weak transcription	Placenta	Placenta
14	chr17:37940400-37941400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr17:37940400-37941600	Strong transcription	Primary B cells from cord blood	blood
16	chr17:37940400-37944000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr17:37940600-37941400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:37940600-37943200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr17:37940800-37941400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:37941000-37941600	Strong transcription	GM12878-XiMat	blood
21	chr17:37941000-37941800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr17:37941000-37942200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr17:37941000-37943600	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr17:37941000-37949400	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr17:37941200-37941400	Strong transcription	Primary T cells from cord blood	blood
26	chr17:37941200-37942000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr17:37941200-37942400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr17:37941200-37942600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr17:37941200-37944400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr17:37941200-37944600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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