Variant report

Variant	rs6735530
Chromosome Location	chr2:46848446-46848447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46846910..46848798-chr2:46875562..46877263,2	K562	blood:
2	chr2:46842719..46845147-chr2:46846797..46849881,4	MCF-7	breast:
3	chr2:46846051..46848798-chr2:46875763..46878074,2	K562	blood:

Variant related genes	Relation type
ENSG00000151665	Chromatin interaction
ENSG00000119878	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1456010	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276554	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs60199254	0.87[ASN][1000 genomes]
rs6749372	0.86[ASN][1000 genomes]
rs7592446	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6735530	CRIPT	cis	Lymphoblastoid	GTEx
rs6735530	CRIPT	cis	lymphoblastoid	seeQTL
rs6735530	LHCGR	cis	cerebellum	SCAN
rs6735530	CRIPT	cis	multi-tissue	Pritchard
rs6735530	CRIPT	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844800-46865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:46844800-46868400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:46844800-46868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:46844800-46868800	Weak transcription	Esophagus	oesophagus
5	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
6	chr2:46845200-46850000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:46845200-46854000	Weak transcription	Colonic Mucosa	Colon
8	chr2:46845400-46854000	Weak transcription	Small Intestine	intestine
9	chr2:46845400-46858400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:46845400-46864800	Weak transcription	Psoas Muscle	Psoas
11	chr2:46845400-46867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
13	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
14	chr2:46845600-46850000	Weak transcription	Fetal Heart	heart
15	chr2:46845600-46854800	Weak transcription	NHEK	skin
16	chr2:46845600-46868200	Weak transcription	Aorta	Aorta
17	chr2:46845600-46868800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:46845800-46849800	Weak transcription	HMEC	breast
19	chr2:46845800-46850000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:46846000-46849400	Strong transcription	Osteobl	bone
21	chr2:46846000-46854400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:46846000-46868600	Weak transcription	Fetal Intestine Small	intestine
23	chr2:46846200-46849000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:46846200-46849000	Strong transcription	Dnd41	blood
25	chr2:46846200-46849400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:46846200-46853400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:46846200-46855200	Strong transcription	Liver	Liver
28	chr2:46846200-46857400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:46846400-46853400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr2:46846400-46853600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:46846400-46853800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:46846400-46853800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:46846400-46853800	Strong transcription	Placenta	Placenta
34	chr2:46846400-46856000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:46846400-46857800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:46846600-46848800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:46846800-46848600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:46846800-46848600	Strong transcription	Colon Smooth Muscle	Colon
39	chr2:46846800-46848600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:46846800-46848600	Strong transcription	Rectal Smooth Muscle	rectum
41	chr2:46846800-46848600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:46846800-46848600	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:46846800-46848600	Strong transcription	Thymus	Thymus
44	chr2:46846800-46848600	Strong transcription	HSMMtube	muscle
45	chr2:46846800-46848600	Strong transcription	HUVEC	blood vessel
46	chr2:46846800-46848600	Strong transcription	NHLF	lung
47	chr2:46846800-46848800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:46846800-46848800	Strong transcription	Primary B cells from cord blood	blood
49	chr2:46846800-46848800	Strong transcription	Primary T cells from cord blood	blood
50	chr2:46846800-46848800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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