Variant report

Variant	rs7122825
Chromosome Location	chr11:73061324-73061325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:73060834..73061439-chr11:73104309..73104871,2	K562	blood:
2	chr11:73061043..73065254-chr11:73095025..73099626,5	MCF-7	breast:
3	chr11:73060033..73062421-chr11:73088511..73090562,2	MCF-7	breast:
4	chr11:73056150..73059125-chr11:73059660..73062281,2	K562	blood:
5	chr11:73018181..73020791-chr11:73060784..73062301,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257038	Chromatin interaction
ENSG00000110237	Chromatin interaction
ENSG00000054967	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1002127	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs10898917	0.91[EUR][1000 genomes]
rs11235770	0.89[CEU][hapmap]
rs11821094	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11823913	0.89[CEU][hapmap]
rs11828904	0.89[CEU][hapmap]
rs12099129	0.83[EUR][1000 genomes]
rs12288753	0.89[CEU][hapmap]
rs12290623	0.89[CEU][hapmap]
rs17244596	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs17244602	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs17310361	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs17851510	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs1892855	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938777	0.89[CEU][hapmap]
rs2027760	1.00[CEU][hapmap]
rs2027761	1.00[CEU][hapmap]
rs2027763	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2298469	0.89[CEU][hapmap]
rs3741149	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs3741151	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741152	1.00[CEU][hapmap]
rs57893472	0.91[EUR][1000 genomes]
rs60078907	1.00[ASN][1000 genomes]
rs61037777	0.96[EUR][1000 genomes]
rs7105681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7107905	0.86[EUR][1000 genomes]
rs7110369	1.00[CHB][hapmap]
rs7114009	0.89[CEU][hapmap]
rs7114376	0.89[CEU][hapmap]
rs7115055	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7115806	1.00[CEU][hapmap]
rs7118982	0.89[CEU][hapmap]
rs7123985	0.89[CEU][hapmap]
rs7125598	0.89[CEU][hapmap]
rs7125949	1.00[CEU][hapmap]
rs7125978	1.00[CEU][hapmap]
rs7129663	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724111	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs73542929	0.81[EUR][1000 genomes]
rs7925226	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7930454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7930880	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs7934218	0.89[CEU][hapmap]
rs7935948	0.89[CEU][hapmap]
rs7938391	0.89[CEU][hapmap]
rs7941359	0.89[CEU][hapmap]
rs7941454	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944346	0.89[CEU][hapmap]
rs7949364	0.96[EUR][1000 genomes]
rs7951072	0.87[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832208	chr11:72876184-73091003	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv520665	chr11:72999221-73061856	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv825993	chr11:73029209-73091929	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv897911	chr11:73044351-73108276	Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7122825	CCND1	cis	cerebellum	SCAN
rs7122825	RELT	cis	lymphoblastoid	seeQTL
rs7122825	LPHN2	trans	lymphoblastoid	seeQTL
rs7122825	P2RY2	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73046600-73061600	Weak transcription	Primary B cells from cord blood	blood
2	chr11:73046600-73075400	Weak transcription	A549	lung
3	chr11:73053800-73064400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:73053800-73065800	Weak transcription	Fetal Kidney	kidney
5	chr11:73053800-73070000	Weak transcription	HUVEC	blood vessel
6	chr11:73054400-73066600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:73054600-73081800	Strong transcription	Fetal Intestine Small	intestine
8	chr11:73054800-73061800	Weak transcription	Pancreas	Pancrea
9	chr11:73054800-73062200	Weak transcription	Liver	Liver
10	chr11:73054800-73063800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:73054800-73072800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:73055000-73071000	Weak transcription	Esophagus	oesophagus
13	chr11:73055000-73072800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:73055000-73072800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:73055200-73063800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:73055800-73066800	Weak transcription	Colonic Mucosa	Colon
17	chr11:73055800-73068400	Weak transcription	NH-A	brain
18	chr11:73055800-73071800	Weak transcription	Brain Substantia Nigra	brain
19	chr11:73056000-73062000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:73056000-73072200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr11:73056000-73077200	Weak transcription	Right Atrium	heart
22	chr11:73056200-73061800	Strong transcription	Fetal Stomach	stomach
23	chr11:73056200-73064200	Weak transcription	NHDF-Ad	bronchial
24	chr11:73056200-73066600	Weak transcription	Brain Angular Gyrus	brain
25	chr11:73056600-73062000	Weak transcription	Fetal Brain Male	brain
26	chr11:73056800-73061800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:73057400-73062000	Strong transcription	Fetal Intestine Large	intestine
28	chr11:73057800-73061800	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:73057800-73062000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:73058000-73062200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:73058000-73071200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr11:73058200-73061600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:73058200-73061600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:73058200-73062000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:73058200-73062000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:73058200-73062200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr11:73058400-73065800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:73058800-73061800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:73058800-73064400	Weak transcription	HSMMtube	muscle
40	chr11:73059000-73062000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:73059000-73062000	Weak transcription	HMEC	breast
42	chr11:73059000-73074000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr11:73059200-73062000	Weak transcription	Brain Anterior Caudate	brain
44	chr11:73059200-73063600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr11:73059200-73063800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr11:73059200-73071400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:73059200-73087400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:73059400-73061800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:73059400-73061800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr11:73059600-73061400	Weak transcription	Brain Cingulate Gyrus	brain

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