Variant report

Variant	rs4332770
Chromosome Location	chr17:37704712-37704713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr17:37703839-37704859	SK-N-SH	brain:	n/a	chr17:37704108-37704122 chr17:37704344-37704358
2	CTCF	chr17:37704700-37704850	WI-38	lung:	n/a	n/a
3	SMC3	chr17:37704038-37704745	GM12878	blood:	n/a	chr17:37704108-37704122 chr17:37704344-37704358
4	CTCF	chr17:37703764-37705244	SK-N-SH	brain:	n/a	chr17:37704344-37704365 chr17:37704107-37704123 chr17:37704343-37704359 chr17:37704106-37704124 chr17:37704342-37704360
5	RAD21	chr17:37703815-37704720	HCT-116	colon:	n/a	chr17:37704344-37704358 chr17:37704343-37704362 chr17:37704546-37704553
6	CTCF	chr17:37703577-37705247	A549	lung:	n/a	chr17:37704344-37704365 chr17:37704107-37704123 chr17:37704343-37704359 chr17:37704106-37704124 chr17:37704342-37704360
7	CTCF	chr17:37704640-37704790	RPTEC	kidney:	n/a	n/a
8	CTCF	chr17:37703603-37704852	HCT-116	colon:	n/a	chr17:37704344-37704365 chr17:37704107-37704123 chr17:37704343-37704359 chr17:37704106-37704124 chr17:37704342-37704360
9	RAD21	chr17:37703714-37704862	SK-N-SH	brain:	n/a	chr17:37704344-37704358 chr17:37704343-37704362 chr17:37704546-37704553
10	CTCF	chr17:37704640-37704790	GM12871	blood:	n/a	n/a
11	CTCF	chr17:37704700-37704850	HCPEpiC	choroid plexus:	n/a	n/a
12	RAD21	chr17:37703820-37704767	HCT-116	colon:	n/a	chr17:37704344-37704358 chr17:37704343-37704362 chr17:37704546-37704553

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37703880..37705005-chr17:38136510..38137377,3	K562	blood:
2	chr17:37704224..37704823-chr17:37731490..37732250,2	K562	blood:

Variant related genes	Relation type
RNU6-233P	TF binding region
CDK12	TF binding region
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1054488	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10775391	0.83[ASN][1000 genomes]
rs1077715	0.83[ASN][1000 genomes]
rs10852933	0.85[ASN][1000 genomes]
rs11078910	0.81[ASN][1000 genomes]
rs11078911	0.81[ASN][1000 genomes]
rs11078912	0.81[ASN][1000 genomes]
rs11078913	0.81[ASN][1000 genomes]
rs11078915	0.86[ASN][1000 genomes]
rs11654018	0.86[ASN][1000 genomes]
rs11655531	0.85[ASN][1000 genomes]
rs11657058	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11657153	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11658219	0.86[ASN][1000 genomes]
rs11658678	0.83[ASN][1000 genomes]
rs12150047	0.83[ASN][1000 genomes]
rs12449852	0.81[ASN][1000 genomes]
rs12450559	0.83[ASN][1000 genomes]
rs12936996	0.81[ASN][1000 genomes]
rs12937013	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938099	0.83[ASN][1000 genomes]
rs12941619	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12942391	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952384	0.81[ASN][1000 genomes]
rs1619021	0.83[ASN][1000 genomes]
rs1874226	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877030	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303316	0.86[ASN][1000 genomes]
rs35335692	0.86[ASN][1000 genomes]
rs364989	0.83[ASN][1000 genomes]
rs3889368	0.83[ASN][1000 genomes]
rs412430	0.83[ASN][1000 genomes]
rs4239222	0.85[ASN][1000 genomes]
rs4357971	0.86[ASN][1000 genomes]
rs439537	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488484	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4591174	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794813	0.81[ASN][1000 genomes]
rs4794814	0.85[ASN][1000 genomes]
rs4795367	0.83[ASN][1000 genomes]
rs4795375	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4795376	0.81[ASN][1000 genomes]
rs4795377	0.81[ASN][1000 genomes]
rs4795379	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795381	0.85[ASN][1000 genomes]
rs4795382	0.84[ASN][1000 genomes]
rs4795384	0.86[ASN][1000 genomes]
rs4795385	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55660616	0.83[ASN][1000 genomes]
rs6503519	0.86[ASN][1000 genomes]
rs6503520	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6503521	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216086	0.86[ASN][1000 genomes]
rs7406928	0.83[ASN][1000 genomes]
rs7503069	0.85[ASN][1000 genomes]
rs7503377	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7503514	0.81[ASN][1000 genomes]
rs7503705	0.81[ASN][1000 genomes]
rs8065963	0.83[ASN][1000 genomes]
rs8067511	0.82[ASN][1000 genomes]
rs8067884	0.81[ASN][1000 genomes]
rs8069074	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8073248	0.87[ASN][1000 genomes]
rs8074276	0.84[ASN][1000 genomes]
rs8074855	0.83[ASN][1000 genomes]
rs8075737	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8081528	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8182252	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903507	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646419	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1057655	chr17:37333956-37732451	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv532712	chr17:37521822-37768345	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv1063848	chr17:37575622-37707592	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4332770	CRKRS	Cis_1M	lymphoblastoid	RTeQTL
rs4332770	PGAP3	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37683800-37719400	Weak transcription	Psoas Muscle	Psoas
2	chr17:37687400-37706600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:37687800-37705000	Weak transcription	NHLF	lung
4	chr17:37687800-37709600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:37687800-37729800	Weak transcription	Small Intestine	intestine
6	chr17:37688000-37707400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:37688400-37705000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr17:37688400-37705600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr17:37688400-37708000	Weak transcription	Gastric	stomach
10	chr17:37688400-37709600	Weak transcription	Colonic Mucosa	Colon
11	chr17:37688400-37711600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr17:37688400-37711600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:37688600-37705200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr17:37689000-37707400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:37689000-37708000	Weak transcription	NH-A	brain
16	chr17:37689000-37719400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr17:37689200-37711600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr17:37690800-37709400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr17:37692000-37704800	Weak transcription	HSMM	muscle
20	chr17:37693000-37719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr17:37693200-37706000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr17:37695400-37727400	Weak transcription	K562	blood
23	chr17:37695600-37707200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:37695800-37707200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr17:37695800-37707400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr17:37695800-37707800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:37695800-37712400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr17:37695800-37723200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr17:37697400-37709600	Weak transcription	HMEC	breast
30	chr17:37699200-37706600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr17:37699800-37705800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:37699800-37706800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr17:37699800-37714800	Strong transcription	Ovary	ovary
34	chr17:37700000-37708000	Weak transcription	Pancreas	Pancrea
35	chr17:37700200-37725800	Strong transcription	Placenta	Placenta
36	chr17:37700400-37705400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr17:37700400-37709600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:37701000-37707000	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr17:37701000-37714600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr17:37701000-37714800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:37701000-37714800	Strong transcription	Brain Anterior Caudate	brain
42	chr17:37701000-37719400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:37701000-37728800	Strong transcription	Liver	Liver
44	chr17:37701200-37706400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr17:37701200-37707400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr17:37701200-37707600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr17:37701200-37708200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr17:37701200-37710600	Strong transcription	Brain Hippocampus Middle	brain
49	chr17:37701200-37727600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr17:37701400-37708200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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