Variant report

Variant	rs12668040
Chromosome Location	chr7:104905057-104905058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:104893338..104895687-chr7:104903857..104906194,3	K562	blood:
2	chr7:104902229..104905190-chr7:104911272..104913681,2	MCF-7	breast:
3	chr7:104903407..104906399-chr7:105027736..105030512,2	MCF-7	breast:
4	chr7:104904327..104906020-chr7:104907361..104909325,2	K562	blood:

Variant related genes	Relation type
ENSG00000135250	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10238507	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs10241415	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10266871	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs10277120	0.83[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs10281422	0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs10281886	0.81[ASN][1000 genomes]
rs10487150	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs10953468	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs10953470	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10953474	0.86[ASN][1000 genomes]
rs1142	0.82[JPT][hapmap]
rs1144	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs11761429	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11765899	0.86[ASN][1000 genomes]
rs11980772	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1204056	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs1204058	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs1204066	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs1204077	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs1204080	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs12334245	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs13235033	0.81[GIH][hapmap];0.87[JPT][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs13238191	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs17721873	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2030776	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2040914	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2057883	0.88[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2057884	0.82[JPT][hapmap]
rs2237612	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237613	0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2237614	0.81[CHB][hapmap]
rs2237617	0.80[JPT][hapmap]
rs2240463	0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2299304	0.93[JPT][hapmap]
rs2299308	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs2299319	0.88[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs35851667	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3779210	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs3801278	0.88[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs3801281	0.88[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs3801282	0.83[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs3801285	0.83[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs3801999	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs41562	0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs41563	0.83[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs4496901	0.88[ASN][1000 genomes]
rs4730070	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs4730072	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs4730073	0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs4730080	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs4730082	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs6466053	0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs6466055	0.83[ASN][1000 genomes]
rs6466056	0.88[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs6466057	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs6466064	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs66599006	0.81[ASN][1000 genomes]
rs6943183	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs6950620	0.93[JPT][hapmap]
rs6962856	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs6967587	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs7357199	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs7789569	0.83[ASN][1000 genomes]
rs7797912	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs7801804	0.82[ASN][1000 genomes]
rs7806591	0.88[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs7811681	0.83[ASN][1000 genomes]
rs917114	0.88[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9640686	0.86[ASN][1000 genomes]
rs9649275	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34588	chr7:104737612-105153242	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2757233	chr7:104758250-105208492	Strong transcription Weak transcription Enhancers Flanking Active TSS 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	39 gene(s)	inside rSNPs	diseases
3	esv2759549	chr7:104758250-105208492	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv8196	chr7:104763559-105155978	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv34580	chr7:104763580-105153242	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2758127	chr7:104766707-105110581	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1028228	chr7:104807207-105182998	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv932138	chr7:104826194-105152816	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1015688	chr7:104849770-105182998	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv888928	chr7:104897964-104944847	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1029832	chr7:104905057-105112489	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12668040	CDHR3	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104869600-104909200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:104879000-104907800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:104885400-104907000	Weak transcription	Fetal Intestine Small	intestine
4	chr7:104886400-104916600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:104891600-104907800	Weak transcription	Aorta	Aorta
6	chr7:104892200-104906600	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:104896400-104909000	Weak transcription	Pancreas	Pancrea
8	chr7:104897000-104905400	Weak transcription	Fetal Brain Male	brain
9	chr7:104897600-104906800	Weak transcription	Right Ventricle	heart
10	chr7:104897600-104907400	Weak transcription	Right Atrium	heart
11	chr7:104898000-104907200	Weak transcription	Fetal Kidney	kidney
12	chr7:104898200-104907200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr7:104898600-104905800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr7:104898600-104909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:104898600-104909000	Weak transcription	Small Intestine	intestine
16	chr7:104898800-104906000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr7:104898800-104906400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr7:104898800-104907800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr7:104898800-104907800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:104899000-104905800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr7:104899000-104906800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:104899400-104907000	Weak transcription	Primary B cells from cord blood	blood
23	chr7:104901800-104905400	Enhancers	Fetal Thymus	thymus
24	chr7:104902200-104905800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:104902200-104906400	Transcr. at gene 5' and 3'	Dnd41	blood
26	chr7:104902400-104906800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:104902600-104905200	Weak transcription	Ovary	ovary
28	chr7:104902600-104905400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:104902600-104905800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:104902600-104906400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:104902600-104907000	Weak transcription	Adipose Nuclei	Adipose
32	chr7:104902600-104907000	Weak transcription	HSMM	muscle
33	chr7:104902600-104907200	Weak transcription	Fetal Heart	heart
34	chr7:104902600-104907200	Weak transcription	NHLF	lung
35	chr7:104902600-104907400	Weak transcription	Hela-S3	cervix
36	chr7:104902600-104907600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:104902600-104907600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:104902600-104907600	Weak transcription	NHDF-Ad	bronchial
39	chr7:104902600-104907800	Weak transcription	Liver	Liver
40	chr7:104902600-104907800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:104902600-104907800	Weak transcription	Osteobl	bone
42	chr7:104902600-104908000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr7:104902800-104905600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr7:104902800-104907200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:104902800-104907200	Weak transcription	HSMMtube	muscle
46	chr7:104902800-104908400	Weak transcription	A549	lung
47	chr7:104903000-104905400	Weak transcription	NHEK	skin
48	chr7:104903000-104906800	Weak transcription	Primary T cells from cord blood	blood
49	chr7:104903000-104907000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr7:104903000-104907200	Weak transcription	Fetal Brain Female	brain

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