Variant report

Variant	rs1153943
Chromosome Location	chr1:223970511-223970512
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223962452..223964542-chr1:223969395..223972147,3	K562	blood:
2	chr1:223970124..223971708-chr1:223972032..223973610,2	K562	blood:
3	chr1:223888774..223890638-chr1:223967678..223970668,2	K562	blood:
4	chr1:223924368..223926769-chr1:223968941..223970904,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAPN2-2	chr1:223970371-223970730	l_201_chr1:223955015-223970728_thyroid

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1153927	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1153928	0.86[ASN][1000 genomes]
rs1153929	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1153930	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1153933	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1153934	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1153936	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1153937	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153938	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153944	0.91[ASN][1000 genomes]
rs1153946	0.89[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1153947	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1153949	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1153950	0.83[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs1153952	0.88[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs1153954	0.84[CHB][hapmap];0.93[ASN][1000 genomes]
rs1153971	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1153973	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1222081	0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs1222120	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1222121	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1222123	0.93[ASN][1000 genomes]
rs1222124	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1222126	0.83[ASN][1000 genomes]
rs1222127	0.86[ASN][1000 genomes]
rs1222128	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1222146	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1222147	0.93[ASN][1000 genomes]
rs1222148	0.89[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1222153	0.83[CHB][hapmap]
rs1222156	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1222158	0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1228475	0.85[ASN][1000 genomes]
rs1538140	0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1621129	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1629850	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16842270	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16842294	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16842321	1.00[CEU][hapmap]
rs17739	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs1981171	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1982610	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1982611	0.84[ASN][1000 genomes]
rs1982612	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1982613	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2242188	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370163	0.91[EUR][1000 genomes]
rs28370164	0.91[EUR][1000 genomes]
rs28370167	0.91[EUR][1000 genomes]
rs28370172	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3738370	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3767709	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3820475	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4653457	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56329085	0.94[EUR][1000 genomes]
rs56918361	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59104475	0.94[EUR][1000 genomes]
rs59196624	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60131749	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60164080	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6658724	0.88[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6667215	0.84[ASN][1000 genomes]
rs6675712	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6687003	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6694214	0.98[EUR][1000 genomes]
rs6698919	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs72749554	0.85[EUR][1000 genomes]
rs72749569	0.89[EUR][1000 genomes]
rs737066	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs750873	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7536779	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:223956800-223974200	Strong transcription	Primary T cells from cord blood	blood
4	chr1:223956800-223974200	Strong transcription	Liver	Liver
5	chr1:223957000-223983400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:223957200-223972800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr1:223959800-223977600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:223960000-223972200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr1:223960200-223971800	Strong transcription	Stomach Smooth Muscle	stomach
10	chr1:223960200-223998600	Strong transcription	Fetal Thymus	thymus
11	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:223960600-223986800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:223960600-223995200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:223960800-223995400	Weak transcription	GM12878-XiMat	blood
16	chr1:223961800-223972200	Strong transcription	Dnd41	blood
17	chr1:223961800-223977200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:223962000-223975000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:223962600-223970600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:223962600-223983600	Weak transcription	Psoas Muscle	Psoas
22	chr1:223962800-223972600	Strong transcription	Primary B cells from cord blood	blood
23	chr1:223963400-223983800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:223964000-223972200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:223964000-223985600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:223964200-223970800	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:223964200-223974200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:223964200-223980000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:223964400-223970600	Weak transcription	Aorta	Aorta
30	chr1:223964400-223972000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:223964400-223972000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:223964400-223972000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:223964400-223972400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:223964400-223972600	Weak transcription	Right Atrium	heart
35	chr1:223964400-223977200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:223964400-223979600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:223964400-224008000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:223964600-223972000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:223964600-223976800	Weak transcription	Stomach Mucosa	stomach
40	chr1:223964600-223977000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:223965000-223973400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:223965400-223970600	Strong transcription	K562	blood
43	chr1:223965400-223970800	Weak transcription	Fetal Heart	heart
44	chr1:223965400-223974200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:223965400-223977200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:223965400-223983800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:223966400-223970600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:223966400-223971000	Weak transcription	HMEC	breast
49	chr1:223966400-223976200	Weak transcription	NHEK	skin
50	chr1:223966600-223983600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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