Variant report

Variant	rs1974745
Chromosome Location	chr17:20059824-20059825
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20059521..20061143-chr17:20081573..20083266,2	MCF-7	breast:
2	chr17:20058693..20060833-chr17:20107962..20111201,3	MCF-7	breast:
3	chr17:19988478..19990422-chr17:20059544..20061745,2	MCF-7	breast:
4	chr17:20057192..20060270-chr17:20108096..20110844,3	K562	blood:
5	chr17:20027673..20031271-chr17:20059449..20061879,3	MCF-7	breast:
6	chr17:19878871..19883594-chr17:20057277..20060362,4	K562	blood:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction
ENSG00000212186	Chromatin interaction
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10491107	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11204300	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11204423	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11653630	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11653869	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11654942	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11657161	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11868116	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11869258	0.84[EUR][1000 genomes]
rs12603372	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12936443	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12938355	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12942568	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12942627	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12949481	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12950564	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1373146	0.84[EUR][1000 genomes]
rs16960697	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1859407	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1992561	0.84[EUR][1000 genomes]
rs2013443	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2042046	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2107565	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2158472	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2189709	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526459	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526463	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2526465	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2526466	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2526476	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526477	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526478	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526481	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526482	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526486	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703770	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2703771	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2703776	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2703777	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2703781	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2703786	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703788	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703795	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703800	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2703803	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2703805	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2703807	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703812	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2703814	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2703819	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850779	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3850780	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925086	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4925087	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925090	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925091	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55705283	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57837691	0.84[EUR][1000 genomes]
rs62066865	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62066870	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587219	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7212500	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7212571	0.80[EUR][1000 genomes]
rs7216599	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7216794	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7219615	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7219908	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7222984	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7222987	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs733794	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs757494	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs757495	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8066143	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8071274	0.84[EUR][1000 genomes]
rs8078716	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8080649	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9893832	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9898080	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9901336	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9901796	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9902032	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9907516	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
4	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
5	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	37 gene(s)	inside rSNPs	diseases
10	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv2003	chr17:20046306-20090653	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	esv3314150	chr17:20058385-20061233	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	esv3314151	chr17:20058385-20061233	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1974745	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20058400-20060000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
2	chr17:20058400-20060200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr17:20058600-20060000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr17:20058600-20060200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:20058600-20060400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr17:20058600-20060400	Active TSS	Duodenum Mucosa	Duodenum
7	chr17:20058800-20060000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:20058800-20060000	Active TSS	Colon Smooth Muscle	Colon
9	chr17:20058800-20060000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
10	chr17:20058800-20060000	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr17:20058800-20060200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr17:20058800-20060200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr17:20058800-20060200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr17:20058800-20060200	Active TSS	Primary T cells from cord blood	blood
15	chr17:20058800-20060200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:20058800-20060200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr17:20058800-20060200	Active TSS	Fetal Intestine Large	intestine
18	chr17:20058800-20060200	Active TSS	Fetal Intestine Small	intestine
19	chr17:20058800-20060200	Active TSS	Rectal Smooth Muscle	rectum
20	chr17:20058800-20060200	Active TSS	Osteobl	bone
21	chr17:20058800-20060400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr17:20058800-20060400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:20058800-20060400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:20058800-20060400	Active TSS	Aorta	Aorta
25	chr17:20058800-20060400	Active TSS	Esophagus	oesophagus
26	chr17:20058800-20060400	Active TSS	Ovary	ovary
27	chr17:20058800-20060400	Active TSS	Placenta Amnion	Placenta Amnion
28	chr17:20058800-20060400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr17:20058800-20060600	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr17:20058800-20060600	Active TSS	Right Atrium	heart
31	chr17:20058800-20060600	Active TSS	HSMM	muscle
32	chr17:20058800-20060800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr17:20058800-20060800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr17:20058800-20060800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr17:20058800-20060800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:20058800-20060800	Active TSS	Brain Anterior Caudate	brain
37	chr17:20058800-20061000	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr17:20058800-20061000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:20058800-20061000	Active TSS	NH-A	brain
40	chr17:20058800-20061200	Active TSS	Brain Angular Gyrus	brain
41	chr17:20058800-20061200	Active TSS	Brain Substantia Nigra	brain
42	chr17:20059000-20060000	Active TSS	Primary B cells from peripheral blood	blood
43	chr17:20059000-20060000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr17:20059000-20060000	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr17:20059000-20060000	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr17:20059000-20060000	Active TSS	Brain Hippocampus Middle	brain
47	chr17:20059000-20060000	Weak transcription	Fetal Heart	heart
48	chr17:20059000-20060000	Active TSS	Fetal Lung	lung
49	chr17:20059000-20060200	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr17:20059000-20060200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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