Variant report

Variant	rs1874226
Chromosome Location	chr17:37729031-37729032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37709600..37711661-chr17:37728844..37731443,2	MCF-7	breast:
2	chr17:37728481..37731764-chr17:37748218..37751803,3	MCF-7	breast:
3	chr17:37728614..37731530-chr17:37739206..37742056,2	MCF-7	breast:
4	chr17:37724500..37726432-chr17:37727779..37730612,3	K562	blood:
5	chr17:37728576..37732593-chr17:37732827..37737352,4	MCF-7	breast:
6	chr17:37724544..37726432-chr17:37727779..37730612,3	K562	blood:
7	chr17:37724265..37726449-chr17:37726824..37730353,3	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10445306	0.87[CHB][hapmap]
rs10491128	0.82[CHB][hapmap]
rs1054488	0.90[AMR][1000 genomes];0.88[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]
rs10852934	0.83[CEU][hapmap]
rs11078898	0.82[CHB][hapmap]
rs11078901	0.82[CHB][hapmap]
rs11078902	0.82[CHB][hapmap]
rs11078906	0.82[CHB][hapmap]
rs11078907	0.80[CHB][hapmap]
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	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs11655531	0.85[ASN][1000 genomes]
rs11657058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11657153	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11657899	0.82[CHB][hapmap]
rs11658219	0.86[ASN][1000 genomes]
rs11658678	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs12150047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs12449852	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs12450559	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs12452509	0.82[CHB][hapmap]
rs12452880	0.82[CHB][hapmap]
rs12600751	0.82[CHB][hapmap]
rs12936996	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs12937013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs12941619	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12942391	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952384	0.81[ASN][1000 genomes]
rs13341996	0.82[CHB][hapmap]
rs1619021	0.83[ASN][1000 genomes]
rs1877030	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303316	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs35335692	0.86[ASN][1000 genomes]
rs364989	0.83[ASN][1000 genomes]
rs3764352	0.83[CEU][hapmap]
rs3889368	0.83[ASN][1000 genomes]
rs412430	0.83[ASN][1000 genomes]
rs4239222	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs4332770	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4357971	0.86[ASN][1000 genomes]
rs439537	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488484	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4511574	0.82[CHB][hapmap]
rs4591174	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794813	0.81[ASN][1000 genomes]
rs4794814	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs4795356	0.82[CHB][hapmap]
rs4795357	0.82[CHB][hapmap]
rs4795358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4795367	0.83[ASN][1000 genomes]
rs4795375	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4795376	0.81[ASN][1000 genomes]
rs4795377	0.81[ASN][1000 genomes]
rs4795379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.90[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	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55660616	0.83[ASN][1000 genomes]
rs6503513	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs6503519	0.86[ASN][1000 genomes]
rs6503520	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6503521	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208252	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7208487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7216086	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs7221875	0.82[CHB][hapmap]
rs7225096	0.82[CHB][hapmap]
rs7406928	0.83[ASN][1000 genomes]
rs7501488	0.82[CHB][hapmap]
rs7503069	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs7503377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7503514	0.81[ASN][1000 genomes]
rs7503705	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs8065963	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs8067511	0.82[ASN][1000 genomes]
rs8067884	0.81[ASN][1000 genomes]
rs8069074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8073248	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8074276	0.84[ASN][1000 genomes]
rs8074855	0.83[ASN][1000 genomes]
rs8075737	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8076546	0.82[CHB][hapmap]
rs8081528	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8182252	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879606	0.83[CEU][hapmap]
rs903507	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs9906612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]

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	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	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
10	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
11	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1874226	PGAP3	cis	Thyroid	GTEx
rs1874226	CRKRS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37687800-37729800	Weak transcription	Small Intestine	intestine
2	chr17:37708800-37729400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:37710400-37729400	Weak transcription	HMEC	breast
4	chr17:37710400-37729600	Weak transcription	NHEK	skin
5	chr17:37710800-37730400	Weak transcription	Stomach Mucosa	stomach
6	chr17:37713000-37729200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr17:37713200-37729600	Weak transcription	NHDF-Ad	bronchial
8	chr17:37714000-37729600	Weak transcription	NHLF	lung
9	chr17:37714600-37729600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr17:37719600-37729600	Weak transcription	HUVEC	blood vessel
11	chr17:37720000-37729600	Weak transcription	NH-A	brain
12	chr17:37720400-37729200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr17:37720400-37729600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:37720400-37730200	Enhancers	Fetal Brain Male	brain
15	chr17:37720600-37729600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:37720600-37729600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:37720800-37729200	Weak transcription	Right Atrium	heart
18	chr17:37721000-37729600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr17:37721000-37729600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr17:37721400-37729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr17:37721400-37729600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr17:37721400-37729600	Weak transcription	Psoas Muscle	Psoas
23	chr17:37721400-37736200	Weak transcription	Fetal Heart	heart
24	chr17:37723400-37729600	Weak transcription	Colon Smooth Muscle	Colon
25	chr17:37723800-37730200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr17:37724000-37729600	Weak transcription	Fetal Kidney	kidney
27	chr17:37724800-37729600	Weak transcription	Brain Hippocampus Middle	brain
28	chr17:37724800-37729600	Weak transcription	Left Ventricle	heart
29	chr17:37724800-37729600	Weak transcription	Osteobl	bone
30	chr17:37725000-37729600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:37725600-37729600	Weak transcription	Ovary	ovary
32	chr17:37725800-37729200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr17:37725800-37729200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:37725800-37729600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:37725800-37729600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr17:37725800-37729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr17:37726000-37729400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:37726000-37729400	Weak transcription	Right Ventricle	heart
39	chr17:37726000-37729600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:37726000-37729600	Weak transcription	Brain Anterior Caudate	brain
41	chr17:37726000-37729800	Weak transcription	Brain Substantia Nigra	brain
42	chr17:37726200-37729200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr17:37726400-37729200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr17:37726400-37729400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:37726400-37729400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:37726400-37729400	Weak transcription	Colonic Mucosa	Colon
47	chr17:37726400-37729600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr17:37726400-37729600	Weak transcription	HSMMtube	muscle
49	chr17:37726600-37729200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr17:37726600-37729200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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