Variant report

Variant	rs7950996
Chromosome Location	chr11:34946712-34946713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34944920..34946901-chr11:34953844..34956335,2	K562	blood:
2	chr11:34936972..34940330-chr11:34946468..34949282,3	K562	blood:
3	chr11:34945269..34946953-chr11:34953904..34955811,2	K562	blood:
4	chr11:34946381..34948541-chr11:34950282..34952383,2	MCF-7	breast:
5	chr11:34941386..34944859-chr11:34946221..34949330,3	K562	blood:
6	chr11:34945262..34947750-chr11:35430544..35432454,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110435	Chromatin interaction
ENSG00000149089	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10488802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10836317	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1117050	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11539202	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11601737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11602364	0.82[AMR][1000 genomes]
rs11602584	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11605600	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11605972	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11605993	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11606580	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11606871	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11607986	0.82[AMR][1000 genomes]
rs11608116	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1409718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17347979	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17348697	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17348711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17349298	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17363135	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17432226	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17433496	0.96[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17434808	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17434946	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17711539	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17783998	0.82[AMR][1000 genomes]
rs17784324	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2217479	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2421744	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3852515	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3852516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3852517	0.92[CEU][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4534556	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55672020	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55868872	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55911702	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55929026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55957800	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56061305	0.81[EUR][1000 genomes]
rs61734605	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7110461	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72912924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72912934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72914758	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs72922479	0.82[AMR][1000 genomes]
rs72922482	0.82[AMR][1000 genomes]
rs72924508	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72924541	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72924562	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72926580	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72928507	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72930433	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72930443	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930458	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930462	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72930468	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72930480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7479823	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7937316	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7948977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv2757436	chr11:34913315-34963728	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759817	chr11:34913315-34963728	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	13 gene(s)	inside rSNPs	diseases
5	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
6	nsv1055116	chr11:34940737-34962291	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv437715	chr11:34941494-34951993	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7950996	APIP	cis	Heart Left Ventricle	GTEx
rs7950996	APIP	cis	Artery Tibial	GTEx
rs7950996	PDHX	cis	cerebellum	SCAN
rs7950996	PDHX	Cis_1M	lymphoblastoid	RTeQTL
rs7950996	APIP	cis	Esophagus Muscularis	GTEx
rs7950996	APIP	cis	Artery Aorta	GTEx
rs7950996	APIP	cis	Nerve Tibial	GTEx
rs7950996	APIP	cis	cerebellum	SCAN
rs7950996	APIP	cis	lymphoblastoid	seeQTL
rs7950996	APIP	cis	Thyroid	GTEx
rs7950996	PDHX	cis	parietal	SCAN
rs7950996	APIP	cis	Adipose Subcutaneous	GTEx
rs7950996	APIP	cis	lung	GTEx
rs7950996	PDHX	cis	lymphoblastoid	seeQTL
rs7950996	APIP	cis	Skin Sun Exposed Lower leg	GTEx
rs7950996	APIP	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34938800-34951400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:34938800-34957400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:34938800-34990400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:34939000-34950600	Weak transcription	Gastric	stomach
5	chr11:34939200-34948000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:34939200-34950000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:34939200-34950200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:34939200-34952200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr11:34939200-34952800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:34939200-34953000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:34939200-34953400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr11:34939200-34956000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:34939200-35000000	Weak transcription	Thymus	Thymus
14	chr11:34939400-34947800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:34939400-34952800	Weak transcription	Primary B cells from cord blood	blood
16	chr11:34939400-34953200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr11:34939400-34953400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:34939600-34947600	Weak transcription	Fetal Kidney	kidney
19	chr11:34939600-34947800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr11:34939600-34949400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:34939600-34949800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:34939600-34950200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:34939600-34962600	Weak transcription	Right Ventricle	heart
24	chr11:34939800-34947400	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:34939800-34949600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr11:34939800-34950800	Weak transcription	Pancreas	Pancrea
27	chr11:34939800-34951200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:34939800-34951400	Weak transcription	Fetal Intestine Small	intestine
29	chr11:34939800-34953800	Weak transcription	Placenta	Placenta
30	chr11:34939800-34960400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr11:34940000-34946800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:34940000-34947800	Weak transcription	HSMM	muscle
33	chr11:34940000-34947800	Weak transcription	HUVEC	blood vessel
34	chr11:34940000-34950800	Weak transcription	Right Atrium	heart
35	chr11:34940000-34954000	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:34940000-34959200	Weak transcription	Fetal Brain Male	brain
37	chr11:34940000-34963800	Weak transcription	Spleen	Spleen
38	chr11:34940200-34946800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:34940200-34947400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:34940200-34947600	Weak transcription	Brain Anterior Caudate	brain
41	chr11:34940200-34947800	Weak transcription	HMEC	breast
42	chr11:34940200-34950000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr11:34940200-34954000	Weak transcription	Primary T cells from cord blood	blood
44	chr11:34940200-34970400	Weak transcription	Left Ventricle	heart
45	chr11:34940200-34984800	Weak transcription	Fetal Stomach	stomach
46	chr11:34940400-34947400	Weak transcription	NHEK	skin
47	chr11:34940400-34947600	Weak transcription	Brain Angular Gyrus	brain
48	chr11:34940400-34948000	Weak transcription	NH-A	brain
49	chr11:34940400-34950200	Weak transcription	Small Intestine	intestine
50	chr11:34940400-34954000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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