Variant report

Variant	rs9895942
Chromosome Location	chr17:38460097-38460098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38458898..38461237-chr17:38499745..38502287,2	K562	blood:
2	chr17:38267756..38269556-chr17:38459898..38462579,2	K562	blood:
3	chr17:38288101..38290586-chr17:38457763..38460423,2	K562	blood:
4	chr17:38457066..38460899-chr17:38504442..38513119,13	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDC6-1	chr17:38459457-38460909	ENSG00000270145.1

Variant related genes	Relation type
ENSG00000188895	Chromatin interaction
ENSG00000131759	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10451257	1.00[MEX][hapmap]
rs11867497	1.00[MEX][hapmap]
rs28631283	0.92[AFR][1000 genomes]
rs28742572	1.00[MEX][hapmap]
rs35163502	1.00[MEX][hapmap]
rs35487582	1.00[MEX][hapmap]
rs9899406	1.00[ASW][hapmap];0.84[LWK][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes]
rs9913992	1.00[MEX][hapmap]

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	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38444800-38462600	Weak transcription	Esophagus	oesophagus
2	chr17:38445600-38460200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:38445600-38462600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr17:38446000-38461000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:38449200-38460200	Strong transcription	HepG2	liver
6	chr17:38450800-38461200	Strong transcription	Dnd41	blood
7	chr17:38452600-38460800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr17:38452600-38461000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:38452800-38461400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr17:38452800-38461400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr17:38453000-38461000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr17:38453000-38462600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr17:38453400-38461200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:38455800-38462800	Weak transcription	Ovary	ovary
15	chr17:38456600-38460600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:38456600-38460800	Strong transcription	GM12878-XiMat	blood
17	chr17:38458600-38460200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:38459000-38460800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
19	chr17:38459000-38461200	Genic enhancers	HMEC	breast
20	chr17:38459000-38461800	Enhancers	NHLF	lung
21	chr17:38459000-38462400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr17:38459000-38465400	Enhancers	Fetal Muscle Leg	muscle
23	chr17:38459000-38465400	Enhancers	Fetal Stomach	stomach
24	chr17:38459200-38460600	Enhancers	Liver	Liver
25	chr17:38459200-38460600	Genic enhancers	A549	lung
26	chr17:38459200-38460800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr17:38459200-38461000	Genic enhancers	NHEK	skin
28	chr17:38459200-38461400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr17:38459200-38461600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:38459200-38462800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:38459200-38465200	Enhancers	Fetal Intestine Large	intestine
32	chr17:38459200-38465400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr17:38459200-38473800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:38459400-38460200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:38459400-38460200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr17:38459400-38460200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr17:38459400-38460200	Enhancers	Brain Hippocampus Middle	brain
38	chr17:38459400-38460200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr17:38459400-38460400	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr17:38459400-38460400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr17:38459400-38460400	Genic enhancers	Thymus	Thymus
42	chr17:38459400-38460400	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr17:38459400-38460600	Enhancers	Primary T cells from cord blood	blood
44	chr17:38459400-38460600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr17:38459400-38460600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr17:38459400-38460600	Enhancers	Brain Substantia Nigra	brain
47	chr17:38459400-38460600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr17:38459400-38460600	Enhancers	Spleen	Spleen
49	chr17:38459400-38460600	Genic enhancers	Hela-S3	cervix
50	chr17:38459400-38460600	Enhancers	HUVEC	blood vessel

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