Variant report

Variant	rs7557998
Chromosome Location	chr2:46714974-46714975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46713674..46717376-chr2:46717590..46719594,3	K562	blood:
2	chr2:46712457..46718126-chr2:46724421..46727428,6	K562	blood:
3	chr2:46714508..46716993-chr2:46724518..46727090,2	K562	blood:
4	chr2:46713674..46716471-chr2:46717649..46719594,2	K562	blood:

Variant related genes	Relation type
ENSG00000253515	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11125077	0.83[AFR][1000 genomes]
rs12470532	0.91[GIH][hapmap]
rs12473626	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12474287	0.91[GIH][hapmap]
rs12619420	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13009087	0.83[AFR][1000 genomes]
rs13017856	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13018019	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13018477	0.88[CEU][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13025174	0.84[CEU][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13032473	0.94[ASW][hapmap];0.84[CEU][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13033917	0.84[CEU][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.83[ASN][1000 genomes]
rs1530627	0.94[ASW][hapmap];0.84[CEU][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs1530628	0.83[ASW][hapmap]
rs1542271	0.84[ASW][hapmap];0.84[CEU][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap]
rs1597041	0.86[AFR][1000 genomes]
rs1868080	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2121697	0.87[CEU][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2197698	0.86[AFR][1000 genomes]
rs2276555	0.89[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3814045	0.91[GIH][hapmap]
rs3814047	0.84[CEU][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4456747	0.86[AFR][1000 genomes]
rs4953381	0.83[AFR][1000 genomes]
rs4953385	0.94[ASW][hapmap];0.84[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4953389	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6715279	0.81[AFR][1000 genomes]
rs6728611	0.92[AFR][1000 genomes]
rs6728847	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6737959	0.94[ASW][hapmap];0.84[CEU][hapmap];0.83[CHD][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs7559484	0.83[MEX][hapmap]
rs7562332	0.88[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7565770	0.94[ASW][hapmap];0.83[CHD][hapmap];0.89[LWK][hapmap]
rs7571742	0.83[MEX][hapmap]
rs7588586	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7588938	0.88[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription 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	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv519216	chr2:46683683-46723219	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv581746	chr2:46699145-46719922	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv581747	chr2:46709571-46718989	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv457341	chr2:46712759-46724016	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv581748	chr2:46712759-46724016	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7557998	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs7557998	CRIPT	cis	parietal	SCAN
rs7557998	CRIPT	cis	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46705000-46716600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:46709600-46715000	Weak transcription	A549	lung
3	chr2:46713600-46717600	Enhancers	Hela-S3	cervix
4	chr2:46713800-46718800	Enhancers	Spleen	Spleen
5	chr2:46714600-46715000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr2:46714600-46715200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:46714600-46715200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:46714600-46715400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr2:46714600-46715400	Enhancers	HUVEC	blood vessel
10	chr2:46714600-46715600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:46714600-46715600	Enhancers	Fetal Stomach	stomach
12	chr2:46714600-46715600	Enhancers	NH-A	brain
13	chr2:46714600-46715800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:46714600-46715800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:46714600-46715800	Enhancers	Stomach Smooth Muscle	stomach
16	chr2:46714600-46715800	Enhancers	HSMM	muscle
17	chr2:46714600-46716000	Enhancers	NHDF-Ad	bronchial
18	chr2:46714600-46716000	Enhancers	Osteobl	bone
19	chr2:46714600-46716200	Enhancers	Psoas Muscle	Psoas
20	chr2:46714600-46718400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:46714600-46718600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:46714600-46718800	Enhancers	Fetal Heart	heart
23	chr2:46714600-46718800	Enhancers	NHLF	lung
24	chr2:46714600-46719200	Enhancers	Left Ventricle	heart
25	chr2:46714800-46715400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr2:46714800-46715400	Enhancers	Fetal Muscle Leg	muscle
27	chr2:46714800-46715600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:46714800-46715600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:46714800-46715600	Enhancers	Aorta	Aorta
30	chr2:46714800-46715600	Enhancers	Brain Hippocampus Middle	brain
31	chr2:46714800-46715600	Enhancers	Lung	lung
32	chr2:46714800-46715600	Enhancers	Ovary	ovary
33	chr2:46714800-46715600	Enhancers	Pancreas	Pancrea
34	chr2:46714800-46715600	Enhancers	HSMMtube	muscle
35	chr2:46714800-46715800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:46714800-46715800	Enhancers	Colon Smooth Muscle	Colon
37	chr2:46714800-46715800	Enhancers	Fetal Muscle Trunk	muscle
38	chr2:46714800-46716000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:46714800-46716000	Enhancers	Placenta	Placenta
40	chr2:46714800-46716000	Enhancers	Right Atrium	heart
41	chr2:46714800-46718000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:46714800-46718000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:46714800-46718600	Enhancers	Right Ventricle	heart
44	chr2:46714800-46718800	Enhancers	Adipose Nuclei	Adipose
45	chr2:46714800-46718800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:46714800-46720800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:46714800-46721600	Enhancers	Cortex derived primary cultured neurospheres	brain

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