Variant report

Variant	rs7572964
Chromosome Location	chr2:32372096-32372097
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:32370490..32374937-chr2:32388646..32392345,4	K562	blood:
2	chr2:32365815..32368775-chr2:32370522..32372496,2	K562	blood:

Variant related genes	Relation type
ENSG00000272716	Chromatin interaction
ENSG00000152683	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10172468	0.91[JPT][hapmap]
rs10208246	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10439444	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs10490360	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs11124274	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs11124275	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs11124278	0.86[ASN][1000 genomes]
rs11676938	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs11678119	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11681731	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11683760	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11683842	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11683931	0.81[AFR][1000 genomes]
rs11689817	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11691939	0.82[CEU][hapmap]
rs11694630	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12465124	0.85[ASN][1000 genomes]
rs12465351	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12474443	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12474598	0.84[ASN][1000 genomes]
rs12478134	0.83[CEU][hapmap]
rs12611678	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12614686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12617289	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12617290	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12618002	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12989936	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs12995952	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12997026	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs13006495	0.82[CEU][hapmap]
rs13007972	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13008192	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13017189	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs13022197	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13427170	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs17011801	0.83[CEU][hapmap]
rs177082	0.83[CEU][hapmap]
rs17767988	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap]
rs212679	0.91[JPT][hapmap]
rs212687	0.86[JPT][hapmap]
rs212689	0.83[CEU][hapmap]
rs212699	0.83[YRI][hapmap]
rs212701	0.83[YRI][hapmap]
rs212703	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs212715	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs212716	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs212717	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs212724	0.84[YRI][hapmap]
rs212737	0.83[YRI][hapmap]
rs212738	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs212739	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs212744	0.91[JPT][hapmap]
rs212745	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs212746	0.80[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs212748	0.91[JPT][hapmap]
rs212751	0.83[CEU][hapmap]
rs212754	0.85[CEU][hapmap]
rs212755	0.91[JPT][hapmap]
rs212758	0.84[CEU][hapmap]
rs212759	0.84[CEU][hapmap]
rs212760	0.80[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs212762	0.95[JPT][hapmap]
rs216544	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2235134	0.80[ASN][1000 genomes]
rs2280967	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2280968	0.82[CEU][hapmap]
rs2280973	0.95[ASN][1000 genomes]
rs2294176	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2294179	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2365555	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap]
rs2365558	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2366736	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2886393	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34197800	0.82[CEU][hapmap]
rs34976640	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35641550	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36014814	0.85[AFR][1000 genomes]
rs375050	0.83[CEU][hapmap]
rs3752916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3752917	0.88[ASN][1000 genomes]
rs3769602	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769603	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769604	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs3769606	1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs385076	0.83[CHB][hapmap]
rs3851308	0.88[ASN][1000 genomes]
rs3851310	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4258846	0.84[ASN][1000 genomes]
rs435572	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs4407291	0.89[ASN][1000 genomes]
rs443609	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4519572	0.89[ASN][1000 genomes]
rs462878	0.82[CEU][hapmap]
rs467523	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs479333	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs4952209	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4952248	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4952249	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4952250	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4952252	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs56208031	0.89[ASN][1000 genomes]
rs6543649	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs659239	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs6716179	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6717209	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6723154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6725184	0.84[CEU][hapmap];0.87[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6737500	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6748621	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6752375	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs6758024	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6760105	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6761417	0.89[ASN][1000 genomes]
rs7561519	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs7566162	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7573543	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7577408	0.86[AFR][1000 genomes]
rs7577696	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7581032	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7581340	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7581432	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7586448	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7588883	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7592239	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7592356	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7601267	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7604289	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7605242	1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][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	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
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv873779	chr2:32330885-32372245	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7572964	NLRC4	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32309800-32381200	Weak transcription	NHDF-Ad	bronchial
2	chr2:32331600-32377400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:32331600-32390200	Weak transcription	Gastric	stomach
4	chr2:32331600-32390200	Weak transcription	Pancreas	Pancrea
5	chr2:32331800-32376400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:32332800-32389400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:32333000-32372400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:32333000-32389800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:32342200-32372400	Weak transcription	Esophagus	oesophagus
10	chr2:32342200-32389800	Weak transcription	Aorta	Aorta
11	chr2:32344200-32389600	Weak transcription	HMEC	breast
12	chr2:32352200-32374600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:32354600-32390200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:32354800-32389600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:32355000-32389800	Weak transcription	Brain Substantia Nigra	brain
16	chr2:32355000-32390200	Weak transcription	Small Intestine	intestine
17	chr2:32355200-32383600	Weak transcription	HSMMtube	muscle
18	chr2:32355400-32389800	Weak transcription	HUVEC	blood vessel
19	chr2:32355600-32389600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:32355600-32389800	Weak transcription	Spleen	Spleen
21	chr2:32356200-32380400	Weak transcription	Colonic Mucosa	Colon
22	chr2:32356400-32383200	Weak transcription	K562	blood
23	chr2:32357400-32389800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:32360000-32390200	Weak transcription	Ovary	ovary
25	chr2:32361000-32377400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:32361000-32377600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:32361000-32389800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:32361200-32374000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:32361200-32375000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:32361200-32375800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:32361200-32381800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:32361200-32383800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:32361200-32389600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:32361200-32389600	Weak transcription	NHEK	skin
35	chr2:32361200-32389600	Weak transcription	Osteobl	bone
36	chr2:32361400-32372800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:32361400-32389600	Weak transcription	Fetal Heart	heart
38	chr2:32361400-32389600	Weak transcription	Hela-S3	cervix
39	chr2:32361600-32389600	Weak transcription	NH-A	brain
40	chr2:32361800-32373200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:32361800-32373600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:32361800-32375200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:32362000-32372400	Strong transcription	Dnd41	blood
44	chr2:32362000-32373400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:32363200-32372200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:32363200-32372600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:32363200-32373000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:32363200-32373200	Weak transcription	Brain Angular Gyrus	brain
49	chr2:32363200-32389600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:32363400-32376600	Weak transcription	Brain Inferior Temporal Lobe	brain

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