Variant report

Variant	rs7942031
Chromosome Location	chr11:47868474-47868475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47792091..47794821-chr11:47867403..47869086,2	K562	blood:
2	chr11:47787394..47789838-chr11:47868299..47871448,5	MCF-7	breast:
3	chr11:47597915..47601799-chr11:47868286..47871887,4	K562	blood:
4	chr11:47787149..47790720-chr11:47868235..47871590,6	MCF-7	breast:
5	chr11:47788106..47790225-chr11:47868385..47869954,2	K562	blood:
6	chr11:47735300..47737622-chr11:47868024..47869979,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200376	Chromatin interaction
ENSG00000231880	Chromatin interaction
ENSG00000165923	Chromatin interaction
ENSG00000109920	Chromatin interaction
ENSG00000123444	Chromatin interaction
ENSG00000213619	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1017875	1.00[CEU][hapmap]
rs11039387	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11819979	0.89[ASN][1000 genomes]
rs11820480	0.92[ASN][1000 genomes]
rs1474056	0.80[ASN][1000 genomes]
rs17791016	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1872167	0.96[ASN][1000 genomes]
rs2138767	0.81[ASN][1000 genomes]
rs2305982	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2305983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[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];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2869531	0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2869532	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4303192	0.80[ASN][1000 genomes]
rs4752786	0.81[ASN][1000 genomes]
rs4752791	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4752805	0.93[CEU][hapmap]
rs4752871	0.95[ASN][1000 genomes]
rs4752872	0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs4752877	1.00[ASN][1000 genomes]
rs4752879	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57436966	0.94[ASN][1000 genomes]
rs58357937	0.89[ASN][1000 genomes]
rs59205786	0.95[ASN][1000 genomes]
rs59652089	0.82[ASN][1000 genomes]
rs60515486	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6485772	0.88[ASN][1000 genomes]
rs6485774	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485783	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs6485784	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6485788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101582	0.87[EUR][1000 genomes]
rs7120737	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7121264	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7123436	1.00[CEU][hapmap]
rs7124949	0.95[ASN][1000 genomes]
rs7130876	0.93[CEU][hapmap];0.89[TSI][hapmap]
rs7924699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7927611	0.95[ASN][1000 genomes]
rs7931089	0.80[ASN][1000 genomes]
rs7945911	0.83[ASN][1000 genomes]
rs7952204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[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	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
4	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7942031	ATG13	cis	parietal	SCAN
rs7942031	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs7942031	LOC441601	cis	cerebellum	SCAN
rs7942031	OR4C3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47796200-47868600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr11:47796600-47868600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr11:47847600-47868800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr11:47851400-47868600	Strong transcription	Placenta	Placenta
6	chr11:47853000-47868600	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr11:47854000-47868600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:47854200-47868600	Strong transcription	HSMM	muscle
9	chr11:47856600-47869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:47862000-47868600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:47864600-47868600	Weak transcription	Stomach Mucosa	stomach
12	chr11:47864600-47868600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:47864800-47868600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:47864800-47868600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
15	chr11:47865000-47869200	Weak transcription	Gastric	stomach
16	chr11:47865400-47869200	Weak transcription	Aorta	Aorta
17	chr11:47865600-47868800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:47865800-47868600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:47865800-47868600	Weak transcription	Colonic Mucosa	Colon
20	chr11:47865800-47868600	Weak transcription	Pancreas	Pancrea
21	chr11:47865800-47868800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:47865800-47869400	Weak transcription	Spleen	Spleen
23	chr11:47866000-47868600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:47866000-47869200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:47866000-47869200	Weak transcription	Esophagus	oesophagus
26	chr11:47866200-47868600	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:47866200-47868600	Weak transcription	Psoas Muscle	Psoas
28	chr11:47866400-47869000	Weak transcription	Right Ventricle	heart
29	chr11:47866400-47869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:47866600-47868600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:47866600-47868800	Genic enhancers	Fetal Thymus	thymus
32	chr11:47866600-47869200	Weak transcription	Left Ventricle	heart
33	chr11:47867000-47868600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr11:47867000-47868600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:47867200-47868600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:47867200-47868600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr11:47867200-47868800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:47867200-47869200	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr11:47867200-47869200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr11:47867400-47868600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr11:47867400-47868600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:47867400-47868600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:47867400-47868600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:47867400-47868600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:47867400-47868800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr11:47867400-47869000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:47867600-47868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:47867600-47868600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr11:47867600-47869200	Enhancers	Primary T cells fromperipheralblood	blood
50	chr11:47867600-47869200	Weak transcription	Lung	lung

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