Variant report

Variant	rs248341
Chromosome Location	chr5:95201703-95201704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95199646..95202540-chr5:95204108..95206460,2	MCF-7	breast:
2	chr5:95199907..95202755-chr5:95294565..95297525,3	MCF-7	breast:
3	chr5:95193159..95197035-chr5:95199083..95201765,3	K562	blood:
4	chr5:95191104..95193650-chr5:95201052..95202970,2	MCF-7	breast:
5	chr5:95201531..95203525-chr5:95206404..95208684,2	K562	blood:

Variant related genes	Relation type
ENSG00000118985	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10476660	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs12659828	0.84[CHD][hapmap]
rs154447	0.81[CEU][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs17085209	0.90[CHB][hapmap];0.91[ASN][1000 genomes]
rs2059209	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs2059210	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs248338	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs248339	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs248340	0.83[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs248342	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6888848	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs248341	CLCNKB	trans	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
2	chr5:95194200-95203000	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr5:95195000-95206400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:95195000-95208400	Weak transcription	Ovary	ovary
5	chr5:95195200-95217400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:95195600-95206200	Weak transcription	Brain Anterior Caudate	brain
7	chr5:95196800-95202000	Enhancers	Fetal Intestine Small	intestine
8	chr5:95196800-95203000	Enhancers	Fetal Intestine Large	intestine
9	chr5:95197000-95201800	Enhancers	Stomach Mucosa	stomach
10	chr5:95197200-95203200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr5:95197800-95204800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:95198200-95202600	Weak transcription	HMEC	breast
13	chr5:95198600-95206200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:95199000-95204200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:95199000-95204200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:95199200-95202000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:95199200-95202600	Weak transcription	NH-A	brain
18	chr5:95199200-95206000	Weak transcription	Fetal Heart	heart
19	chr5:95199400-95202000	Weak transcription	GM12878-XiMat	blood
20	chr5:95199400-95203200	Enhancers	Osteobl	bone
21	chr5:95199400-95203400	Weak transcription	Fetal Thymus	thymus
22	chr5:95199400-95204000	Weak transcription	Primary T cells from cord blood	blood
23	chr5:95199400-95204000	Weak transcription	Dnd41	blood
24	chr5:95199400-95204400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr5:95199400-95204400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:95199400-95205000	Weak transcription	HUVEC	blood vessel
27	chr5:95199400-95205200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:95199400-95210000	Weak transcription	Right Ventricle	heart
29	chr5:95199600-95202200	Weak transcription	Primary B cells from cord blood	blood
30	chr5:95199600-95204600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:95200000-95201800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:95200000-95202800	Weak transcription	HSMM	muscle
33	chr5:95200000-95203200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:95200000-95206000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:95200000-95206200	Weak transcription	Esophagus	oesophagus
36	chr5:95200000-95206200	Weak transcription	Psoas Muscle	Psoas
37	chr5:95200200-95202400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:95200400-95205200	Weak transcription	Adipose Nuclei	Adipose
39	chr5:95200800-95202000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:95200800-95205400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:95201000-95201800	Enhancers	Brain Substantia Nigra	brain
42	chr5:95201000-95202000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr5:95201000-95202200	Weak transcription	NHEK	skin
44	chr5:95201000-95202600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:95201000-95205400	Weak transcription	Liver	Liver
46	chr5:95201000-95205800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:95201200-95201800	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr5:95201200-95202200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:95201200-95202200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr5:95201200-95202200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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