Variant report

Variant	rs28799952
Chromosome Location	chr17:37533056-37533057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37526319..37527863-chr17:37532918..37534625,2	K562	blood:
2	chr17:37531290..37534298-chr17:37556765..37559429,3	K562	blood:
3	chr17:37529412..37533173-chr17:37556280..37559153,3	K562	blood:

Variant related genes	Relation type
ENSG00000108306	Chromatin interaction
ENSG00000266469	Chromatin interaction

Extended variants
information (count: 155 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10221223	0.82[ASN][1000 genomes]
rs10491128	0.83[ASN][1000 genomes]
rs11078894	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11078895	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11078898	0.86[ASN][1000 genomes]
rs11078899	0.82[EUR][1000 genomes]
rs11655972	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11869109	0.85[ASN][1000 genomes]
rs11869259	0.85[ASN][1000 genomes]
rs11869323	0.86[ASN][1000 genomes]
rs11871813	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150047	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12150493	0.80[ASN][1000 genomes]
rs12449852	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12452509	0.80[ASN][1000 genomes]
rs12600625	0.81[ASN][1000 genomes]
rs12600751	0.83[ASN][1000 genomes]
rs12938099	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12938268	0.80[ASN][1000 genomes]
rs12941418	0.82[EUR][1000 genomes]
rs12950186	0.83[EUR][1000 genomes]
rs13341996	0.86[ASN][1000 genomes]
rs1971663	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2302073	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2338797	0.83[ASN][1000 genomes]
rs2338798	0.85[ASN][1000 genomes]
rs2338799	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2338800	0.82[ASN][1000 genomes]
rs28482878	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2879258	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2879259	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34432983	0.83[ASN][1000 genomes]
rs34597616	0.82[ASN][1000 genomes]
rs35285898	0.83[ASN][1000 genomes]
rs35546703	0.86[ASN][1000 genomes]
rs3744349	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4287601	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4410117	0.80[ASN][1000 genomes]
rs4511574	0.86[ASN][1000 genomes]
rs4516267	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4794807	0.86[ASN][1000 genomes]
rs4794808	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795356	0.85[ASN][1000 genomes]
rs4795357	0.82[ASN][1000 genomes]
rs4795358	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4795359	0.80[ASN][1000 genomes]
rs4795367	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57399933	0.85[ASN][1000 genomes]
rs57933226	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs582088	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs582176	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs584377	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs587880	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs590051	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs594794	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs597069	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs649180	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6503500	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6503502	0.82[ASN][1000 genomes]
rs6503503	0.85[ASN][1000 genomes]
rs6503504	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6503506	0.86[ASN][1000 genomes]
rs6503507	0.86[ASN][1000 genomes]
rs6503513	0.82[ASN][1000 genomes]
rs651827	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs665413	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs667193	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs667239	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68178216	0.86[ASN][1000 genomes]
rs7208252	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7208274	0.85[ASN][1000 genomes]
rs7208487	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7208714	0.86[ASN][1000 genomes]
rs7210488	0.86[ASN][1000 genomes]
rs7212621	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215983	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7218074	0.86[ASN][1000 genomes]
rs7218484	0.81[ASN][1000 genomes]
rs7218670	0.82[ASN][1000 genomes]
rs7220650	0.82[ASN][1000 genomes]
rs7221117	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7221875	0.86[ASN][1000 genomes]
rs7223331	0.82[ASN][1000 genomes]
rs7223438	0.86[ASN][1000 genomes]
rs73293051	0.85[ASN][1000 genomes]
rs7359658	0.81[ASN][1000 genomes]
rs7405667	0.80[ASN][1000 genomes]
rs7501488	0.80[ASN][1000 genomes]
rs7503081	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs801417	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs801418	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801427	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801429	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8065879	0.86[ASN][1000 genomes]
rs8066704	0.82[ASN][1000 genomes]
rs8067302	0.82[ASN][1000 genomes]
rs8067511	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8067948	0.82[ASN][1000 genomes]
rs8068427	0.83[ASN][1000 genomes]
rs8070695	0.82[ASN][1000 genomes]
rs8071300	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8072351	0.80[ASN][1000 genomes]
rs8073511	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8073907	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8074276	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8074855	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8076494	0.86[ASN][1000 genomes]
rs8076546	0.83[ASN][1000 genomes]
rs8077104	0.86[ASN][1000 genomes]
rs8078599	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8079303	0.86[ASN][1000 genomes]
rs8079560	0.82[ASN][1000 genomes]
rs8081033	0.83[ASN][1000 genomes]
rs9646419	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9747983	0.81[ASN][1000 genomes]
rs9890198	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9891892	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9892055	0.83[ASN][1000 genomes]
rs9892675	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9893735	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9894500	0.86[ASN][1000 genomes]
rs9894586	0.82[ASN][1000 genomes]
rs9894864	0.83[ASN][1000 genomes]
rs9896913	0.86[ASN][1000 genomes]
rs9898170	0.85[ASN][1000 genomes]
rs9898773	0.86[ASN][1000 genomes]
rs9899069	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9901219	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9903363	0.82[ASN][1000 genomes]
rs9904919	0.82[ASN][1000 genomes]
rs9905432	0.83[ASN][1000 genomes]
rs9905617	0.82[ASN][1000 genomes]
rs9906612	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9908131	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908760	0.82[ASN][1000 genomes]
rs9909064	0.82[ASN][1000 genomes]
rs9909304	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9912212	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9912310	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9944411	0.82[ASN][1000 genomes]
rs9944459	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	nsv1057470	chr17:37135183-37549816	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv543339	chr17:37135183-37549816	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	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
4	nsv1060126	chr17:37333956-37659189	Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv908204	chr17:37349655-37682657	Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv1057057	chr17:37395082-37627025	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1055612	chr17:37409865-37563236	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28799952	CRKRS	Cis_1M	lymphoblastoid	RTeQTL
rs28799952	PGAP3	cis	Thyroid	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37496400-37534000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:37498200-37534200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:37498600-37541200	Weak transcription	Fetal Thymus	thymus
4	chr17:37498600-37543800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:37498600-37544000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr17:37498800-37556400	Weak transcription	Thymus	Thymus
7	chr17:37499200-37544000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:37509000-37543000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr17:37514800-37556200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr17:37515400-37555600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr17:37515600-37543200	Weak transcription	Fetal Intestine Large	intestine
12	chr17:37517600-37535600	Weak transcription	Psoas Muscle	Psoas
13	chr17:37517600-37536400	Weak transcription	Brain Anterior Caudate	brain
14	chr17:37517600-37555200	Weak transcription	Brain Germinal Matrix	brain
15	chr17:37517600-37556600	Weak transcription	Fetal Muscle Leg	muscle
16	chr17:37518000-37554800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:37521000-37541400	Weak transcription	Right Atrium	heart
18	chr17:37521200-37541400	Weak transcription	Lung	lung
19	chr17:37521200-37544400	Weak transcription	Placenta	Placenta
20	chr17:37522400-37534400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr17:37522400-37535800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr17:37522600-37546800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr17:37522600-37555400	Weak transcription	Fetal Lung	lung
24	chr17:37522600-37556200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr17:37522800-37535800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:37522800-37554800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:37522800-37555400	Weak transcription	Adipose Nuclei	Adipose
28	chr17:37522800-37556400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr17:37523000-37535800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr17:37523200-37536400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr17:37523200-37546800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr17:37523400-37556200	Weak transcription	Ovary	ovary
33	chr17:37523600-37555800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:37527400-37535600	Weak transcription	Fetal Intestine Small	intestine
35	chr17:37527400-37535600	Weak transcription	Fetal Stomach	stomach
36	chr17:37529800-37536400	Weak transcription	Colon Smooth Muscle	Colon
37	chr17:37529800-37544000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:37530000-37534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:37530000-37543200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr17:37530200-37555600	Weak transcription	Primary T cells from cord blood	blood
41	chr17:37530800-37534000	Weak transcription	Gastric	stomach
42	chr17:37531400-37534600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:37532600-37533200	Enhancers	Primary B cells from peripheral blood	blood
44	chr17:37532600-37533200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:37532600-37533200	Enhancers	Left Ventricle	heart
46	chr17:37532600-37533400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr17:37532600-37534400	Enhancers	GM12878-XiMat	blood
48	chr17:37532600-37534800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr17:37532600-37534800	Enhancers	HMEC	breast
50	chr17:37532600-37535000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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