Variant report

Variant	rs7938962
Chromosome Location	chr11:34964636-34964637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34960896..34963192-chr11:34963561..34965150,2	K562	blood:
2	chr11:34937811..34940525-chr11:34962659..34964952,2	MCF-7	breast:
3	chr11:34937287..34939092-chr11:34964143..34965972,2	K562	blood:

Variant related genes	Relation type
ENSG00000149089	Chromatin interaction
ENSG00000110435	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10488801	1.00[JPT][hapmap]
rs10488803	1.00[JPT][hapmap]
rs10488804	1.00[JPT][hapmap]
rs10488806	0.82[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1049306	1.00[JPT][hapmap]
rs1049307	1.00[JPT][hapmap]
rs11032927	1.00[JPT][hapmap]
rs11032937	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11032938	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11032940	1.00[JPT][hapmap]
rs11032941	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11032942	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11032943	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11032966	0.81[ASN][1000 genomes]
rs11500297	1.00[JPT][hapmap]
rs11500298	1.00[EUR][1000 genomes]
rs12273153	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12273271	1.00[JPT][hapmap]
rs12275620	1.00[JPT][hapmap]
rs12275911	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12276735	1.00[JPT][hapmap]
rs12278245	1.00[JPT][hapmap]
rs12279549	0.81[ASN][1000 genomes]
rs12280293	0.81[ASN][1000 genomes]
rs12283472	1.00[EUR][1000 genomes]
rs12283652	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12283763	1.00[JPT][hapmap]
rs12285752	0.86[JPT][hapmap]
rs12286538	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288594	1.00[JPT][hapmap]
rs12292363	0.81[ASN][1000 genomes]
rs12292719	0.88[JPT][hapmap]
rs12293733	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12294125	1.00[JPT][hapmap]
rs12295452	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs16926295	0.97[EUR][1000 genomes]
rs17435469	0.81[ASN][1000 genomes]
rs2901525	0.97[EUR][1000 genomes]
rs3763926	1.00[JPT][hapmap]
rs3763929	0.86[JPT][hapmap]
rs3763931	1.00[JPT][hapmap]
rs3763933	1.00[JPT][hapmap]
rs3763934	1.00[JPT][hapmap]
rs3763937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3794165	1.00[JPT][hapmap]
rs3794170	1.00[JPT][hapmap]
rs3794172	1.00[EUR][1000 genomes]
rs3818393	1.00[JPT][hapmap]
rs3818401	1.00[JPT][hapmap]
rs4417241	0.81[ASN][1000 genomes]
rs6484746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7102259	1.00[JPT][hapmap]
rs7104943	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7104984	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7110223	1.00[JPT][hapmap]
rs7111607	1.00[JPT][hapmap]
rs7113708	1.00[JPT][hapmap]
rs7116411	0.86[JPT][hapmap]
rs7119958	0.88[JPT][hapmap]
rs7126659	1.00[JPT][hapmap]
rs7129830	1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7931454	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7941930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7947650	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7952208	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832119	chr11:34815528-35009370	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2754010	chr11:34940724-35001024	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7938962	APIP	cis	Muscle Skeletal	GTEx
rs7938962	APIP	cis	Esophagus Mucosa	GTEx
rs7938962	APIP	cis	Esophagus Muscularis	GTEx
rs7938962	APIP	cis	Thyroid	GTEx
rs7938962	APIP	cis	lung	GTEx
rs7938962	APIP	cis	Artery Tibial	GTEx
rs7938962	APIP	cis	uninvolved skin	skin_eQTL
rs7938962	APIP	cis	Adipose Subcutaneous	GTEx
rs7938962	APIP	cis	Heart Left Ventricle	GTEx
rs7938962	APIP	cis	Whole Blood	GTEx
rs7938962	APIP	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34938800-34990400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:34939200-35000000	Weak transcription	Thymus	Thymus
3	chr11:34940200-34970400	Weak transcription	Left Ventricle	heart
4	chr11:34940200-34984800	Weak transcription	Fetal Stomach	stomach
5	chr11:34948000-34990600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr11:34948000-35000400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:34948000-35006800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:34948200-34997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr11:34948600-34990400	Weak transcription	HUVEC	blood vessel
10	chr11:34948800-34965000	Weak transcription	HSMM	muscle
11	chr11:34949200-34990400	Weak transcription	NHEK	skin
12	chr11:34950400-34991600	Weak transcription	NHLF	lung
13	chr11:34951000-34965200	Weak transcription	Gastric	stomach
14	chr11:34951000-34970400	Weak transcription	Aorta	Aorta
15	chr11:34951000-34970400	Weak transcription	Ovary	ovary
16	chr11:34951000-34981400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:34951400-34986600	Weak transcription	Fetal Thymus	thymus
18	chr11:34951600-34992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:34951800-34970400	Weak transcription	Pancreas	Pancrea
20	chr11:34951800-34985000	Weak transcription	Lung	lung
21	chr11:34951800-34988200	Weak transcription	Fetal Intestine Small	intestine
22	chr11:34951800-35000200	Weak transcription	Psoas Muscle	Psoas
23	chr11:34952200-35010800	Weak transcription	Small Intestine	intestine
24	chr11:34952400-34990200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:34953600-34965000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:34954400-34969400	Weak transcription	Fetal Lung	lung
27	chr11:34954600-34965200	Weak transcription	Primary B cells from cord blood	blood
28	chr11:34954600-34978800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:34954600-34986600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:34954600-34987800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:34954600-34991200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:34954800-34988200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:34955000-34969600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:34955000-34988200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:34955200-34969600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:34955400-34965800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:34955400-34970400	Weak transcription	Liver	Liver
38	chr11:34955400-34985200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:34955400-34989000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr11:34955800-34979200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:34955800-34981200	Weak transcription	Brain Anterior Caudate	brain
42	chr11:34955800-34985000	Weak transcription	Placenta	Placenta
43	chr11:34956000-34966800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr11:34956000-34969600	Weak transcription	Brain Angular Gyrus	brain
45	chr11:34956200-34968200	Weak transcription	Primary T cells from cord blood	blood
46	chr11:34956200-34980800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr11:34956400-34990600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr11:34956800-34969000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:34958000-34965200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:34958000-34965200	Weak transcription	Fetal Muscle Leg	muscle

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