Variant report

Variant	rs6758024
Chromosome Location	chr2:32294486-32294487
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32290727..32292444-chr2:32293437..32296073,2	MCF-7	breast:
2	chr2:32294423..32296947-chr2:32389682..32392119,3	K562	blood:
3	chr2:32286904..32290628-chr2:32293788..32299321,9	MCF-7	breast:
4	chr2:32288481..32290380-chr2:32294426..32296430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152683	Chromatin interaction
ENSG00000272716	Chromatin interaction
ENSG00000021574	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10208246	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs10439444	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10490360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124274	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11124275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124276	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11124277	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11676938	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs11678119	0.84[CEU][hapmap];0.95[CHB][hapmap];0.81[YRI][hapmap]
rs11681731	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11683931	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11686061	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11691879	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12465124	0.85[ASN][1000 genomes]
rs12465351	1.00[CHB][hapmap]
rs12474443	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12611678	0.83[ASN][1000 genomes]
rs12614686	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12617289	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12617290	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12618002	0.82[ASN][1000 genomes]
rs12620922	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1272585	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs12989936	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12992743	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12997026	1.00[CHB][hapmap]
rs13000753	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13007972	0.84[ASN][1000 genomes]
rs13008192	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13017189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13022197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13024004	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13029752	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033833	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13427170	1.00[CHB][hapmap]
rs13431540	0.86[ASN][1000 genomes]
rs160797	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs160801	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17767988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs212679	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs212699	0.94[CEU][hapmap]
rs212701	0.94[CEU][hapmap]
rs212703	0.91[CHB][hapmap]
rs212715	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[YRI][hapmap]
rs212716	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[YRI][hapmap]
rs212717	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs212724	0.95[CEU][hapmap]
rs212726	0.95[CEU][hapmap]
rs212727	0.94[CEU][hapmap]
rs212730	0.94[CEU][hapmap]
rs212731	0.94[CEU][hapmap]
rs212737	0.89[CEU][hapmap]
rs212738	1.00[CHB][hapmap]
rs212739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs212745	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs212746	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs212758	1.00[CEU][hapmap]
rs212759	1.00[CEU][hapmap]
rs212760	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs212762	0.81[JPT][hapmap]
rs216538	0.91[ASN][1000 genomes]
rs216544	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2235134	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280969	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294176	0.81[ASN][1000 genomes]
rs2294179	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2365555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2365558	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2366297	0.86[CHB][hapmap]
rs2366736	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs34856365	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35650265	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36014814	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3752916	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs3752917	0.81[ASN][1000 genomes]
rs3769602	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs3769604	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769606	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs385076	0.83[CHB][hapmap]
rs3851308	0.81[ASN][1000 genomes]
rs3851310	0.84[CEU][hapmap]
rs430759	0.94[CEU][hapmap]
rs435572	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs443609	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs454119	0.92[ASN][1000 genomes]
rs455060	0.94[CEU][hapmap]
rs467523	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs469305	0.86[CEU][hapmap];0.85[ASN][1000 genomes]
rs479333	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4952209	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4952247	0.84[EUR][1000 genomes]
rs4952248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap]
rs4952249	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952252	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs56208031	0.82[ASN][1000 genomes]
rs56740303	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6543647	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543649	0.84[EUR][1000 genomes]
rs659239	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs660393	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67157050	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6716179	0.91[CHB][hapmap]
rs6717209	1.00[CHB][hapmap]
rs6723154	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6725184	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[YRI][hapmap]
rs6737500	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6738349	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6747488	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6748621	0.89[CEU][hapmap];0.90[CHB][hapmap];0.96[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749336	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6752375	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6760105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6761417	0.82[ASN][1000 genomes]
rs678251	0.91[ASN][1000 genomes]
rs72862234	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7370704	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7559964	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7561519	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7566162	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7572964	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7573543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7575139	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7577408	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7577696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7581032	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7581340	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7581432	1.00[CHB][hapmap]
rs7586448	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7588883	0.95[CHB][hapmap]
rs7600173	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7600885	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7601267	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7604559	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7605242	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7608127	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7608229	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9677104	0.85[ASN][1000 genomes]
rs9750659	0.86[ASN][1000 genomes]
rs9752631	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv820001	chr2:32293362-32297072	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv828698	chr2:32293493-32296584	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6758024	NLRC4	cis	Lymphoblastoid	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32289600-32330800	Weak transcription	Spleen	Spleen
2	chr2:32289800-32297000	Weak transcription	Psoas Muscle	Psoas
3	chr2:32289800-32298400	Weak transcription	Small Intestine	intestine
4	chr2:32289800-32304000	Weak transcription	Ovary	ovary
5	chr2:32289800-32313800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:32289800-32314600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:32289800-32315800	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:32289800-32319400	Weak transcription	Aorta	Aorta
9	chr2:32289800-32319400	Weak transcription	Pancreas	Pancrea
10	chr2:32289800-32330800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:32290000-32297400	Weak transcription	Osteobl	bone
12	chr2:32290000-32299600	Weak transcription	Thymus	Thymus
13	chr2:32290000-32315800	Weak transcription	Fetal Kidney	kidney
14	chr2:32290000-32315800	Weak transcription	HSMM	muscle
15	chr2:32290000-32316600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:32290000-32318600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:32290200-32295400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:32290200-32313800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:32290200-32330800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:32290400-32297400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:32290400-32298200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:32290400-32304000	Weak transcription	Adipose Nuclei	Adipose
23	chr2:32290400-32313400	Weak transcription	Fetal Thymus	thymus
24	chr2:32290400-32313800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:32290400-32315000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:32290400-32315000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:32290400-32315000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:32290400-32331000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:32290400-32353400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:32290600-32295200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:32290600-32314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:32290600-32330800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:32290800-32294800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:32290800-32295600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:32290800-32295800	Strong transcription	Fetal Stomach	stomach
36	chr2:32290800-32299000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:32290800-32313600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:32290800-32313800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:32290800-32317200	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:32290800-32330200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:32291000-32295200	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:32291000-32295600	Weak transcription	Brain Substantia Nigra	brain
43	chr2:32291000-32298400	Weak transcription	Primary T cells from cord blood	blood
44	chr2:32291000-32299000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:32291000-32301600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:32291000-32304200	Weak transcription	GM12878-XiMat	blood
47	chr2:32291000-32314800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:32291000-32330400	Weak transcription	Brain Anterior Caudate	brain
49	chr2:32291000-32330800	Weak transcription	Brain Angular Gyrus	brain
50	chr2:32291000-32332600	Weak transcription	A549	lung

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