Variant report

Variant	rs7396439
Chromosome Location	chr11:9228785-9228786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr11:9228028-9228971	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr11:9227899-9228812	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9227494..9229881-chr11:9482227..9483923,2	K562	blood:

Variant related genes	Relation type
DENND5A	TF binding region
ENSG00000166478	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10770000	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10770001	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10770002	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10770003	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10770004	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10770006	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs10770008	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap]
rs10770010	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap]
rs10770016	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10840196	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11042182	0.82[TSI][hapmap]
rs11042200	0.95[YRI][hapmap]
rs11042227	0.93[ASN][1000 genomes]
rs11042245	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042252	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11042267	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap]
rs11608172	0.94[ASN][1000 genomes]
rs12289113	0.93[ASN][1000 genomes]
rs12295767	0.89[ASN][1000 genomes]
rs12296016	0.94[ASN][1000 genomes]
rs12420463	0.86[ASN][1000 genomes]
rs12577661	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2133216	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2873069	0.92[ASN][1000 genomes]
rs34729888	0.93[ASN][1000 genomes]
rs35686957	0.81[EUR][1000 genomes]
rs35757766	0.86[ASN][1000 genomes]
rs35955530	0.94[ASN][1000 genomes]
rs4369406	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs4447178	0.81[EUR][1000 genomes]
rs5014247	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs61877814	0.93[ASN][1000 genomes]
rs61877916	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6486206	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6486210	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6486215	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6486226	0.93[ASN][1000 genomes]
rs6486231	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7101432	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7104221	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7109911	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7112540	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7114688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7115062	0.93[ASN][1000 genomes]
rs7116459	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs7121013	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap]
rs7123342	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs71476818	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7394878	0.95[YRI][hapmap]
rs7482630	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs770	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7924664	0.93[ASN][1000 genomes]
rs7925308	0.95[YRI][hapmap]
rs7930507	0.95[YRI][hapmap]
rs7933448	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7941520	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952374	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs9736263	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9888193	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9888229	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1053045	chr11:9208881-9363488	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv540947	chr11:9208881-9363488	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7396439	CCKBR	cis	cerebellum	SCAN
rs7396439	MRPL17	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9162000-9230600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:9169600-9238000	Weak transcription	Esophagus	oesophagus
3	chr11:9171800-9230200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:9172000-9230400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:9182400-9231800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr11:9199800-9230400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:9200600-9229000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:9200600-9230400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:9201000-9230800	Weak transcription	HMEC	breast
10	chr11:9202600-9251200	Weak transcription	Small Intestine	intestine
11	chr11:9221600-9229200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:9223600-9230800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:9224000-9232600	Weak transcription	Colonic Mucosa	Colon
14	chr11:9225400-9236800	Weak transcription	Primary B cells from cord blood	blood
15	chr11:9225600-9229000	Weak transcription	Fetal Intestine Large	intestine
16	chr11:9225600-9229800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:9225600-9230800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr11:9225600-9232400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:9225800-9229000	Weak transcription	Fetal Intestine Small	intestine
20	chr11:9225800-9229400	Weak transcription	Brain Angular Gyrus	brain
21	chr11:9225800-9229600	Weak transcription	K562	blood
22	chr11:9225800-9229800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:9225800-9230200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:9225800-9230200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:9225800-9230200	Weak transcription	Fetal Thymus	thymus
26	chr11:9225800-9230400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:9225800-9230400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr11:9225800-9230400	Weak transcription	Ovary	ovary
29	chr11:9225800-9230400	Weak transcription	Psoas Muscle	Psoas
30	chr11:9225800-9230400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:9225800-9230400	Weak transcription	Right Ventricle	heart
32	chr11:9225800-9230600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:9225800-9230600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:9225800-9230800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:9225800-9231200	Weak transcription	NHEK	skin
36	chr11:9225800-9232000	Weak transcription	Spleen	Spleen
37	chr11:9225800-9234400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr11:9225800-9236200	Weak transcription	Thymus	Thymus
39	chr11:9225800-9237800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:9225800-9237800	Weak transcription	Gastric	stomach
41	chr11:9226000-9229000	Weak transcription	GM12878-XiMat	blood
42	chr11:9226000-9229600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:9226000-9229800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:9226000-9229800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr11:9226000-9230200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr11:9226000-9230200	Weak transcription	Brain Germinal Matrix	brain
47	chr11:9226000-9230400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:9226000-9230400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr11:9226000-9230400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr11:9226000-9230800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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