Variant report

Variant	rs11695952
Chromosome Location	chr2:47262695-47262696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47243930..47246637-chr2:47261701..47264377,2	MCF-7	breast:
2	chr2:47261315..47264096-chr2:47264626..47268326,4	K562	blood:
3	chr2:47260087..47265958-chr2:47400378..47404964,8	K562	blood:
4	chr2:47262016..47264669-chr2:47272967..47274595,2	MCF-7	breast:
5	chr2:47252232..47263251-chr2:47397787..47406051,20	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALM2-1	chr2:47262418-47262764	ENSG00000233845.1

Variant related genes	Relation type
ENSG00000233845	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12617529	0.87[MEX][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes]
rs1865257	0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4245812	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952863	0.83[MEX][hapmap]
rs4953449	0.84[EUR][1000 genomes]
rs6731476	0.88[EUR][1000 genomes]
rs892378	0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs892379	0.86[AMR][1000 genomes];0.82[EUR][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	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
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984532	chr2:47237908-47270533	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv457363	chr2:47249239-47263232	Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv581753	chr2:47249239-47263232	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv528091	chr2:47249239-47273732	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47232000-47265000	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:47245800-47268600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:47246000-47283800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:47246800-47281600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:47247400-47263000	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:47251600-47265000	Strong transcription	Primary T cells from cord blood	blood
10	chr2:47251600-47266000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:47252000-47283400	Strong transcription	Thymus	Thymus
12	chr2:47253400-47263000	Genic enhancers	Esophagus	oesophagus
13	chr2:47255600-47273400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:47256800-47264000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:47257000-47277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:47257400-47262800	Enhancers	Psoas Muscle	Psoas
17	chr2:47257600-47265200	Genic enhancers	Spleen	Spleen
18	chr2:47257600-47267800	Genic enhancers	Fetal Muscle Leg	muscle
19	chr2:47257800-47262800	Genic enhancers	Fetal Stomach	stomach
20	chr2:47258400-47268400	Genic enhancers	Fetal Thymus	thymus
21	chr2:47258400-47282600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:47258600-47263400	Enhancers	Liver	Liver
23	chr2:47258600-47263400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr2:47258600-47265200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:47258800-47263200	Enhancers	HUVEC	blood vessel
26	chr2:47258800-47263400	Enhancers	Left Ventricle	heart
27	chr2:47259000-47263000	Genic enhancers	Duodenum Mucosa	Duodenum
28	chr2:47259000-47263200	Genic enhancers	Rectal Mucosa Donor 29	rectum
29	chr2:47259000-47263200	Enhancers	Right Atrium	heart
30	chr2:47259000-47263200	Enhancers	NH-A	brain
31	chr2:47259000-47263800	Enhancers	Fetal Heart	heart
32	chr2:47259200-47263200	Enhancers	Fetal Lung	lung
33	chr2:47259200-47263200	Enhancers	Stomach Mucosa	stomach
34	chr2:47259200-47263400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:47259200-47263400	Genic enhancers	Fetal Intestine Small	intestine
36	chr2:47259200-47263400	Enhancers	Fetal Kidney	kidney
37	chr2:47259200-47263600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:47259200-47265000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr2:47259400-47263000	Enhancers	Brain Anterior Caudate	brain
40	chr2:47259400-47263400	Enhancers	Right Ventricle	heart
41	chr2:47259400-47265000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:47259400-47266800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:47259600-47263200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:47259600-47263400	Enhancers	Colon Smooth Muscle	Colon
45	chr2:47259600-47263400	Enhancers	Pancreas	Pancrea
46	chr2:47259600-47295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:47259800-47263600	Enhancers	Fetal Intestine Large	intestine
48	chr2:47260000-47266000	Enhancers	Placenta	Placenta
49	chr2:47260200-47262800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr2:47260200-47263000	Enhancers	Ovary	ovary

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