Variant report

Variant	rs6727038
Chromosome Location	chr2:55540745-55540746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55540693..55542535-chr2:55543595..55545823,2	K562	blood:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10169395	0.81[YRI][hapmap]
rs10189439	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10194425	0.85[YRI][hapmap]
rs1047948	0.88[CEU][hapmap]
rs10496042	0.83[AFR][1000 genomes]
rs11125567	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11680143	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11692239	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11892007	0.80[YRI][hapmap]
rs12105731	0.80[YRI][hapmap]
rs12470528	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12471421	0.93[JPT][hapmap]
rs12476508	0.83[ASN][1000 genomes]
rs12476548	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12617887	0.82[AFR][1000 genomes]
rs12621289	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs12621495	0.81[YRI][hapmap]
rs12713292	0.90[ASN][1000 genomes]
rs12713293	0.80[YRI][hapmap]
rs12713295	0.82[YRI][hapmap]
rs13013113	0.80[YRI][hapmap]
rs13019339	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs13022424	0.80[AFR][1000 genomes]
rs1344881	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1370360	0.82[YRI][hapmap]
rs1437387	0.80[YRI][hapmap]
rs1437388	0.80[YRI][hapmap]
rs1437394	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1545555	0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1902059	0.82[ASN][1000 genomes]
rs1902060	0.80[YRI][hapmap]
rs1982484	0.83[ASN][1000 genomes]
rs1982485	0.82[ASN][1000 genomes]
rs1992127	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1992128	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2576687	0.90[ASN][1000 genomes]
rs2576704	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2576705	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2576706	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2576707	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2576713	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2576714	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2576715	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2576716	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2576717	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589055	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2589056	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2589059	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2589065	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2589066	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2589072	0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2589073	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2589075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2589077	0.94[JPT][hapmap]
rs2589084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs2589085	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2589086	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2589087	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2589088	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2589090	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2589091	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2589102	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2589103	0.92[ASN][1000 genomes]
rs2589105	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2589106	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2864828	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2864829	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2864830	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2867174	0.82[YRI][hapmap]
rs2867180	0.81[ASN][1000 genomes]
rs2867181	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2903508	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2917776	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2917778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2920964	0.83[ASN][1000 genomes]
rs2920971	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2920974	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2966467	0.90[ASN][1000 genomes]
rs3099075	0.88[ASN][1000 genomes]
rs3099076	0.85[ASN][1000 genomes]
rs3099077	0.90[ASN][1000 genomes]
rs3099079	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3099082	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3099084	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3111404	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3111410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3111411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3111412	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3111413	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35963448	0.90[ASN][1000 genomes]
rs3762510	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3791633	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3791634	0.96[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3791652	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs3791653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4349381	0.90[ASN][1000 genomes]
rs4672039	0.84[JPT][hapmap]
rs55711116	0.82[ASN][1000 genomes]
rs55828034	0.83[ASN][1000 genomes]
rs55908714	0.85[ASN][1000 genomes]
rs56133422	0.81[ASN][1000 genomes]
rs57410428	0.86[ASN][1000 genomes]
rs62137151	0.90[ASN][1000 genomes]
rs62137154	0.86[ASN][1000 genomes]
rs62137157	0.85[ASN][1000 genomes]
rs6545487	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545488	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545493	0.88[JPT][hapmap]
rs66507139	0.83[EUR][1000 genomes]
rs6706178	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6724338	0.82[AFR][1000 genomes]
rs6725124	0.91[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6726732	0.80[YRI][hapmap]
rs6747649	0.80[YRI][hapmap]
rs6754930	0.82[AFR][1000 genomes]
rs7558687	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs7561473	0.81[AFR][1000 genomes]
rs7564292	0.91[ASN][1000 genomes]
rs7570934	0.85[ASN][1000 genomes]
rs7575929	0.92[ASN][1000 genomes]
rs7576695	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7582580	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7586529	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7600339	0.85[AFR][1000 genomes]
rs7603216	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9789365	0.82[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6727038	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
4	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
7	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
8	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
9	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:55511200-55542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
14	chr2:55512600-55546000	Weak transcription	Small Intestine	intestine
15	chr2:55514800-55549600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:55515800-55550400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
19	chr2:55520000-55541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:55523000-55548000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
25	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:55523600-55541000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:55523600-55542000	Weak transcription	Fetal Brain Male	brain
28	chr2:55523600-55548000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:55523800-55541000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:55524000-55541200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:55524800-55543200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:55524800-55549400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:55526400-55549600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:55527000-55546400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:55527400-55541000	Weak transcription	Brain Anterior Caudate	brain
37	chr2:55528600-55542000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:55529400-55544400	Weak transcription	Placenta	Placenta
39	chr2:55532200-55543800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:55533000-55542000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:55533000-55544000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
43	chr2:55534800-55544200	Strong transcription	Liver	Liver
44	chr2:55535200-55549600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:55535200-55549600	Strong transcription	Dnd41	blood
46	chr2:55535400-55546400	Strong transcription	HepG2	liver
47	chr2:55535400-55548000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:55535400-55550200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:55536400-55548400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:55537000-55541400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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