Variant report

Variant	rs4392104
Chromosome Location	chr17:37700917-37700918
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	POLR2A	chr17:37700869-37701043	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr17:37699889-37701385	K562	blood:	n/a	n/a

Variant related genes	Relation type
CDK12	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10775391	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1077715	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10852933	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11078905	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11078906	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11078907	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11078910	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11078911	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11078912	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11078913	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11078915	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11654018	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11654853	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11654935	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11655531	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11658219	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11658678	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12450559	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12936996	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12952384	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1619021	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2018026	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2303316	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35335692	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs364989	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3889368	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs412430	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4239222	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4357971	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4794813	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4794814	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4795376	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4795377	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4795381	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4795382	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4795384	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55660616	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6503518	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6503519	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7216086	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7219909	0.85[AFR][1000 genomes]
rs7225096	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7405770	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7406928	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7503069	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7503514	0.82[ASN][1000 genomes]
rs7503705	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8065963	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8067884	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8182252	0.81[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4392104	CRKRS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37660600-37704400	Weak transcription	Stomach Mucosa	stomach
2	chr17:37675400-37704000	Weak transcription	Right Atrium	heart
3	chr17:37683800-37703000	Weak transcription	Fetal Brain Male	brain
4	chr17:37683800-37719400	Weak transcription	Psoas Muscle	Psoas
5	chr17:37685600-37702600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr17:37687400-37702800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:37687400-37704000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:37687400-37706600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:37687800-37701000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:37687800-37701200	Weak transcription	Aorta	Aorta
11	chr17:37687800-37701200	Weak transcription	Left Ventricle	heart
12	chr17:37687800-37701400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr17:37687800-37701400	Weak transcription	Colon Smooth Muscle	Colon
14	chr17:37687800-37702800	Weak transcription	Right Ventricle	heart
15	chr17:37687800-37702800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr17:37687800-37702800	Weak transcription	Spleen	Spleen
17	chr17:37687800-37703600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:37687800-37705000	Weak transcription	NHLF	lung
19	chr17:37687800-37709600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:37687800-37729800	Weak transcription	Small Intestine	intestine
21	chr17:37688000-37701000	Weak transcription	Brain Anterior Caudate	brain
22	chr17:37688000-37701000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr17:37688000-37702800	Weak transcription	Brain Germinal Matrix	brain
24	chr17:37688000-37707400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr17:37688400-37701200	Weak transcription	Brain Angular Gyrus	brain
26	chr17:37688400-37701200	Weak transcription	Brain Hippocampus Middle	brain
27	chr17:37688400-37701400	Weak transcription	Brain Substantia Nigra	brain
28	chr17:37688400-37701400	Weak transcription	Thymus	Thymus
29	chr17:37688400-37702800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr17:37688400-37703800	Weak transcription	Esophagus	oesophagus
31	chr17:37688400-37703800	Weak transcription	Fetal Kidney	kidney
32	chr17:37688400-37703800	Weak transcription	NHEK	skin
33	chr17:37688400-37704600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr17:37688400-37705000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr17:37688400-37705600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr17:37688400-37708000	Weak transcription	Gastric	stomach
37	chr17:37688400-37709600	Weak transcription	Colonic Mucosa	Colon
38	chr17:37688400-37711600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr17:37688400-37711600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr17:37688600-37701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:37688600-37705200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr17:37688800-37703800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr17:37689000-37702800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:37689000-37703000	Weak transcription	A549	lung
45	chr17:37689000-37704400	Weak transcription	Fetal Brain Female	brain
46	chr17:37689000-37707400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:37689000-37708000	Weak transcription	NH-A	brain
48	chr17:37689000-37719400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr17:37689200-37701200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr17:37689200-37702800	Weak transcription	NHDF-Ad	bronchial

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