Variant report

Variant	rs6746104
Chromosome Location	chr2:55639023-55639024
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55633136..55639027-chr2:55639441..55643745,9	K562	blood:
2	chr2:55638580..55640592-chr2:55645857..55648376,2	MCF-7	breast:
3	chr2:55458173..55459835-chr2:55636615..55639548,2	K562	blood:

Variant related genes	Relation type
ENSG00000143947	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10169061	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10169395	0.87[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10172058	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10187983	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10191937	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194425	0.90[CHB][hapmap];0.85[YRI][hapmap]
rs1045613	0.80[CEU][hapmap]
rs10496042	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11125564	0.85[AMR][1000 genomes]
rs11125571	0.81[ASN][1000 genomes]
rs11125573	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11678347	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11886931	0.83[EUR][1000 genomes]
rs11891739	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs11902837	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12614357	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12617887	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12621289	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12621495	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12623605	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713293	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713294	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713295	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713296	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713298	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12991401	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13001912	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13010237	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13010255	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13013113	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13019339	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13022424	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13028925	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13389156	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13423775	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1349884	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1349885	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1370360	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1370361	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1437394	0.86[YRI][hapmap]
rs1902060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1992127	0.81[YRI][hapmap]
rs2198575	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2589085	0.86[YRI][hapmap]
rs2589087	0.81[YRI][hapmap]
rs2867174	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2867175	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2867176	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2867177	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28672687	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920971	0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs3111404	0.86[YRI][hapmap]
rs3111413	0.83[YRI][hapmap]
rs36052911	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3791642	0.91[CHB][hapmap]
rs3791650	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs3791652	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3828235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56978967	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66882175	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6724338	0.91[CHB][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6747649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6752182	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6754930	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6756777	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74181227	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7558687	0.86[CEU][hapmap];0.90[CHB][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs7561473	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7569535	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7572492	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7589390	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7600339	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7604067	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7606505	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9789365	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6746104	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
3	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
4	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
5	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
8	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
10	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
11	chr2:55624400-55645600	Weak transcription	Ovary	ovary
12	chr2:55628600-55646000	Weak transcription	Esophagus	oesophagus
13	chr2:55630400-55645800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:55630600-55644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:55630800-55642400	Weak transcription	Pancreas	Pancrea
16	chr2:55630800-55644800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:55630800-55645200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:55630800-55645200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:55631000-55645400	Weak transcription	Placenta	Placenta
20	chr2:55631200-55642600	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:55631400-55642600	Weak transcription	Right Ventricle	heart
22	chr2:55631600-55639200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:55631800-55645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:55632000-55644800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:55632600-55645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:55632800-55639200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:55632800-55640000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:55632800-55645800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:55633000-55639400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:55633000-55645000	Weak transcription	Liver	Liver
31	chr2:55633000-55645800	Weak transcription	Fetal Intestine Small	intestine
32	chr2:55633000-55645800	Weak transcription	Spleen	Spleen
33	chr2:55633000-55646000	Weak transcription	Lung	lung
34	chr2:55633200-55639400	Weak transcription	Adipose Nuclei	Adipose
35	chr2:55633200-55639400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:55633200-55644800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:55633400-55639400	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:55633800-55639400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:55633800-55639400	Weak transcription	Left Ventricle	heart
40	chr2:55634000-55639200	Weak transcription	Hela-S3	cervix
41	chr2:55635400-55639600	Enhancers	Brain Angular Gyrus	brain
42	chr2:55636200-55644200	Weak transcription	Fetal Heart	heart
43	chr2:55636400-55642400	Weak transcription	Fetal Brain Female	brain
44	chr2:55636400-55642600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:55636600-55639200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:55636600-55639200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:55636600-55639200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:55636600-55640200	Weak transcription	NHDF-Ad	bronchial
49	chr2:55636600-55641000	Strong transcription	Fetal Thymus	thymus
50	chr2:55636600-55643200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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