Variant report

Variant	rs17640616
Chromosome Location	chr1:228411255-228411256
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228407306..228411999-chr1:228412295..228415050,4	K562	blood:
2	chr1:228407306..228411999-chr1:228412295..228416286,6	K562	blood:
3	chr1:228404999..228407013-chr1:228410390..228412165,2	MCF-7	breast:

Extended variants
information (count: 135 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1059778	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs10753445	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs10799471	0.83[EUR][1000 genomes]
rs10916268	0.87[TSI][hapmap]
rs10916277	0.86[EUR][1000 genomes]
rs11584385	0.84[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs11799681	0.83[EUR][1000 genomes]
rs11804508	0.84[EUR][1000 genomes]
rs12024649	0.83[EUR][1000 genomes]
rs12084338	1.00[CEU][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12097591	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12130630	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12134624	0.88[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs12564763	0.87[TSI][hapmap]
rs12726781	0.84[EUR][1000 genomes]
rs12745416	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1331303	0.85[EUR][1000 genomes]
rs1411910	0.84[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs1411911	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557026	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1620111	0.84[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1629290	0.86[EUR][1000 genomes]
rs1629294	0.84[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1636195	0.82[ASW][hapmap];1.00[JPT][hapmap]
rs1745413	0.82[ASW][hapmap]
rs1757129	0.86[EUR][1000 genomes]
rs1757132	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1757133	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1757138	0.83[EUR][1000 genomes]
rs1757139	0.84[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1757140	0.86[EUR][1000 genomes]
rs1757141	0.86[EUR][1000 genomes]
rs1757142	0.80[EUR][1000 genomes]
rs1757144	0.84[EUR][1000 genomes]
rs1757145	0.87[EUR][1000 genomes]
rs1757147	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1757148	0.85[EUR][1000 genomes]
rs1757149	0.84[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs1757150	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1757151	0.87[EUR][1000 genomes]
rs1757152	0.84[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1757155	0.86[EUR][1000 genomes]
rs1757156	0.84[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs1757158	0.87[EUR][1000 genomes]
rs17623766	0.89[EUR][1000 genomes]
rs1771459	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1771460	0.84[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1771461	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs1771462	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs1771467	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1771468	0.83[EUR][1000 genomes]
rs1771469	0.84[EUR][1000 genomes]
rs1771470	0.84[EUR][1000 genomes]
rs1771471	0.84[EUR][1000 genomes]
rs1771472	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs1771474	0.84[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1771476	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1771477	0.86[EUR][1000 genomes]
rs1771478	0.86[EUR][1000 genomes]
rs1771479	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1771482	0.84[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs1771483	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1771484	0.91[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs1771485	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1771487	0.81[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2066237	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs2298014	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2313600	0.89[EUR][1000 genomes]
rs2313601	0.84[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs2313602	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs2776845	0.85[EUR][1000 genomes]
rs2776853	0.84[EUR][1000 genomes]
rs2776855	0.84[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2776856	0.84[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs2792984	0.85[EUR][1000 genomes]
rs2872538	0.84[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs3121191	0.80[EUR][1000 genomes]
rs3121192	0.82[EUR][1000 genomes]
rs3795777	0.84[EUR][1000 genomes]
rs3795782	0.88[TSI][hapmap]
rs3795809	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs41303079	0.86[EUR][1000 genomes]
rs4653543	0.85[EUR][1000 genomes]
rs4653545	0.83[EUR][1000 genomes]
rs4653907	0.84[EUR][1000 genomes]
rs4653917	1.00[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4653919	0.85[EUR][1000 genomes]
rs4653920	0.86[EUR][1000 genomes]
rs4653921	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4653931	0.86[EUR][1000 genomes]
rs4653933	0.85[EUR][1000 genomes]
rs4653943	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4653951	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs489926	0.82[EUR][1000 genomes]
rs491293	0.83[EUR][1000 genomes]
rs493945	0.85[TSI][hapmap]
rs512406	0.83[EUR][1000 genomes]
rs545313	0.83[EUR][1000 genomes]
rs546967	0.83[EUR][1000 genomes]
rs55658545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55873533	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs55971985	0.84[EUR][1000 genomes]
rs56112646	0.84[EUR][1000 genomes]
rs566640	0.83[EUR][1000 genomes]
rs61825279	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827540	0.86[EUR][1000 genomes]
rs6426492	0.96[CEU][hapmap]
rs6657968	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6661539	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6673893	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6682260	1.00[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs72757811	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72757812	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72757824	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72757827	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72757829	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7512209	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs7525075	0.83[EUR][1000 genomes]
rs7532141	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532924	0.84[CEU][hapmap]
rs7537636	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs7539762	1.00[CEU][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs849749	0.83[TSI][hapmap]
rs947087	0.84[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][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	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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 miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
11	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17640616	DUSP5P	cis	parietal	SCAN
rs17640616	MRPL55	cis	parietal	SCAN
rs17640616	WDR26	cis	cerebellum	SCAN
rs17640616	OBSCN	cis	Esophagus Mucosa	GTEx
rs17640616	ITPKB	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228401400-228412200	Weak transcription	HSMMtube	muscle
2	chr1:228401400-228412600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:228401600-228412200	Weak transcription	Right Atrium	heart
4	chr1:228401800-228412000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:228402000-228412000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:228402000-228412200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:228402000-228412200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:228402000-228412600	Weak transcription	Fetal Kidney	kidney
9	chr1:228402200-228411800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:228402200-228412200	Weak transcription	A549	lung
11	chr1:228402200-228412200	Weak transcription	Hela-S3	cervix
12	chr1:228402200-228412200	Weak transcription	NHEK	skin
13	chr1:228402200-228412400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:228402200-228412600	Weak transcription	Primary B cells from cord blood	blood
15	chr1:228402200-228415200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:228402400-228411400	Strong transcription	Fetal Intestine Small	intestine
19	chr1:228402400-228411600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:228402400-228412400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:228402400-228412600	Weak transcription	HMEC	breast
22	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
23	chr1:228402800-228411800	Weak transcription	Esophagus	oesophagus
24	chr1:228402800-228412600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:228403000-228412200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:228403000-228412200	Weak transcription	Colonic Mucosa	Colon
27	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:228403200-228418000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:228403400-228415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:228404200-228411600	Strong transcription	Fetal Stomach	stomach
31	chr1:228404200-228412000	Weak transcription	Brain Anterior Caudate	brain
32	chr1:228404200-228412200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:228404200-228412600	Weak transcription	Fetal Brain Male	brain
34	chr1:228404400-228411800	Weak transcription	Pancreas	Pancrea
35	chr1:228404800-228412000	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:228407600-228411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:228407600-228412200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:228407600-228412200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:228408000-228411800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:228408000-228411800	Weak transcription	Fetal Intestine Large	intestine
41	chr1:228408000-228412200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:228408200-228411800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:228408200-228411800	Weak transcription	Fetal Thymus	thymus
44	chr1:228408200-228411800	Weak transcription	Ovary	ovary
45	chr1:228408200-228412000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:228408200-228412200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:228408200-228412200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:228408200-228412200	Weak transcription	Psoas Muscle	Psoas
49	chr1:228408400-228411600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:228408400-228411800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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