Variant report

Variant	rs1357636
Chromosome Location	chr1:85869042-85869043
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85866495..85869056-chr1:86046414..86047968,2	K562	blood:

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1006989	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs10489510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10747318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873702	0.88[CEU][hapmap]
rs11161607	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1146383	0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs12022248	0.98[ASN][1000 genomes]
rs12029221	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12033483	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12034249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035116	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12038426	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12042780	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12047189	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1261681	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1342323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1357635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1523994	0.88[CEU][hapmap]
rs1523995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608537	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17388696	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965876	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975755	0.88[CEU][hapmap]
rs2016104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037594	0.83[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs2064510	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124140	0.84[ASN][1000 genomes]
rs2300633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389948	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851268	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4428939	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512701	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4631749	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949889	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949897	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4949898	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4949899	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs499869	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs539714	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs600098	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs604974	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs631817	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6420965	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659070	0.93[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6672870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722663	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72722671	0.90[ASN][1000 genomes]
rs72722691	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72722692	0.94[AMR][1000 genomes]
rs72724608	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs731194	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7515261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7539738	0.89[EUR][1000 genomes]
rs7555670	0.83[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs990916	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking 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 miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3393958	chr1:85857980-85874598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1357636	CLCA4	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85845000-85870000	Weak transcription	HSMMtube	muscle
2	chr1:85855200-85870000	Weak transcription	Fetal Stomach	stomach
3	chr1:85856000-85872800	Weak transcription	Fetal Intestine Small	intestine
4	chr1:85862200-85874600	Weak transcription	Pancreas	Pancrea
5	chr1:85864000-85872600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:85864400-85869800	Weak transcription	Aorta	Aorta
7	chr1:85864400-85870600	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:85864400-85871000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:85864400-85871800	Weak transcription	NH-A	brain
10	chr1:85864400-85872200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:85864400-85873000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:85864400-85874600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:85864600-85870000	Weak transcription	Brain Anterior Caudate	brain
14	chr1:85864800-85876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:85865200-85870000	Weak transcription	Psoas Muscle	Psoas
16	chr1:85865200-85871200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:85865400-85869200	Weak transcription	HUVEC	blood vessel
18	chr1:85865400-85870800	Weak transcription	NHDF-Ad	bronchial
19	chr1:85865400-85871200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:85865400-85871400	Weak transcription	Fetal Lung	lung
21	chr1:85865400-85871400	Weak transcription	HSMM	muscle
22	chr1:85865400-85872800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:85865600-85869800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:85865600-85870800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:85865600-85871600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:85865800-85869800	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:85865800-85870200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:85866200-85870800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:85866200-85871000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:85866200-85871000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:85866200-85871600	Weak transcription	Adipose Nuclei	Adipose
32	chr1:85866600-85870000	Weak transcription	Ovary	ovary
33	chr1:85866800-85870000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:85868600-85869200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:85868600-85870800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:85868600-85872800	Enhancers	Liver	Liver
37	chr1:85868800-85869400	Weak transcription	Osteobl	bone
38	chr1:85869000-85869200	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:85869000-85869200	Enhancers	Fetal Kidney	kidney
40	chr1:85869000-85870400	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:85869000-85871200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:85869000-85872800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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