Variant report

Variant	rs169413
Chromosome Location	chr17:19849745-19849746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19849218..19850772-chr17:19856829..19859320,2	K562	blood:
2	chr17:19830891..19833677-chr17:19848474..19850191,2	K562	blood:
3	chr17:19848718..19850427-chr17:19878972..19881942,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108599	Chromatin interaction
ENSG00000266126	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12449662	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12450857	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453720	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943369	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12944084	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12946508	0.87[ASN][1000 genomes]
rs1638526	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1638527	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1638528	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17604987	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17605101	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668529	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203449	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs203454	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203464	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs203467	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203474	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs203475	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203476	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203478	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203480	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2108981	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34182788	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34726000	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35254155	0.81[AMR][1000 genomes]
rs35315252	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35925051	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35979784	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36097967	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403021	0.90[EUR][1000 genomes]
rs427033	0.88[EUR][1000 genomes]
rs4577147	0.87[ASN][1000 genomes]
rs4925054	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4925055	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4925063	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925064	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56005410	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066267	0.81[AMR][1000 genomes]
rs62066345	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62066346	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066347	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066348	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066349	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066350	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066351	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066352	0.81[AMR][1000 genomes]
rs62067482	0.87[ASN][1000 genomes]
rs62067483	0.87[ASN][1000 genomes]
rs6813	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7209653	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8079923	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs850622	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9891503	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9901294	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs169413	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
3	chr17:19804000-19853000	Strong transcription	Dnd41	blood
4	chr17:19825200-19851800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:19827600-19851600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:19827600-19852800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:19830600-19851200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:19831600-19851400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr17:19838600-19851600	Weak transcription	Psoas Muscle	Psoas
10	chr17:19839800-19849800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:19840000-19851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
13	chr17:19841600-19852800	Strong transcription	Primary B cells from cord blood	blood
14	chr17:19841800-19851600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:19841800-19852600	Strong transcription	Fetal Intestine Large	intestine
16	chr17:19842000-19850000	Weak transcription	Gastric	stomach
17	chr17:19842000-19850000	Weak transcription	Pancreas	Pancrea
18	chr17:19842000-19852600	Strong transcription	Hela-S3	cervix
19	chr17:19842400-19850000	Weak transcription	Aorta	Aorta
20	chr17:19842400-19851800	Strong transcription	Primary hematopoietic stem cells	blood
21	chr17:19842600-19851600	Strong transcription	GM12878-XiMat	blood
22	chr17:19843000-19850000	Weak transcription	Right Ventricle	heart
23	chr17:19844600-19849800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr17:19844600-19849800	Weak transcription	HUVEC	blood vessel
25	chr17:19844600-19850000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr17:19844600-19850000	Weak transcription	NH-A	brain
27	chr17:19844600-19851400	Weak transcription	Brain Substantia Nigra	brain
28	chr17:19844600-19851600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr17:19844600-19851800	Weak transcription	Small Intestine	intestine
30	chr17:19844600-19859200	Weak transcription	NHDF-Ad	bronchial
31	chr17:19844800-19851000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr17:19844800-19851600	Weak transcription	Fetal Heart	heart
33	chr17:19844800-19853000	Strong transcription	HepG2	liver
34	chr17:19844800-19859600	Weak transcription	HSMMtube	muscle
35	chr17:19844800-19861000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr17:19845200-19849800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr17:19845200-19857200	Weak transcription	Fetal Kidney	kidney
38	chr17:19845400-19857000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr17:19846000-19852200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr17:19846200-19850000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:19846200-19850200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr17:19846200-19851000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr17:19846200-19852000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr17:19846200-19852000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr17:19846400-19851600	Strong transcription	Fetal Muscle Leg	muscle
46	chr17:19846400-19851600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr17:19846400-19851800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr17:19846400-19852200	Strong transcription	Liver	Liver
49	chr17:19846400-19852400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr17:19846600-19850000	Weak transcription	Brain Anterior Caudate	brain

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