Variant report

Variant	rs11121489
Chromosome Location	chr1:9823784-9823785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9821662..9824159-chr1:9828181..9830598,2	K562	blood:
2	chr1:9815045..9817854-chr1:9822064..9824472,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10779730	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779731	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10864436	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs10864437	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10864438	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11121484	0.87[AMR][1000 genomes]
rs11121485	0.86[EUR][1000 genomes]
rs11121486	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes]
rs11121488	0.86[EUR][1000 genomes]
rs11121490	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11121492	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs11121493	0.85[CEU][hapmap]
rs11674	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11804356	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806520	0.90[ASN][1000 genomes]
rs12021914	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12037599	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs12042293	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes]
rs12047054	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12064975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078414	0.85[CEU][hapmap];0.80[YRI][hapmap]
rs12088273	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1220419	0.82[ASN][1000 genomes]
rs12568720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12569008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1615629	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[ASN][1000 genomes]
rs1660741	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1660742	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17034335	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs1767277	0.85[CEU][hapmap];0.90[YRI][hapmap]
rs4512653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845975	0.82[ASN][1000 genomes]
rs56109009	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6666296	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs6677664	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6699320	0.85[CEU][hapmap]
rs72855716	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7526958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7550246	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7550295	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs767762	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv827364	chr1:9822732-9825197	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9801200-9837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:9801400-9854200	Weak transcription	Fetal Kidney	kidney
3	chr1:9804400-9836600	Weak transcription	Small Intestine	intestine
4	chr1:9804600-9836600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:9806400-9825800	Weak transcription	HSMMtube	muscle
6	chr1:9810000-9832400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:9810200-9825800	Weak transcription	NHDF-Ad	bronchial
8	chr1:9810200-9826000	Weak transcription	Hela-S3	cervix
9	chr1:9810200-9826000	Weak transcription	HSMM	muscle
10	chr1:9810200-9829200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:9810400-9825800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:9811600-9832400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:9811600-9832400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:9811800-9832400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:9811800-9857000	Weak transcription	Aorta	Aorta
16	chr1:9812000-9826200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:9812400-9832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:9812600-9829000	Weak transcription	Stomach Mucosa	stomach
19	chr1:9812800-9831000	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:9813400-9829000	Weak transcription	Colonic Mucosa	Colon
21	chr1:9813400-9830400	Weak transcription	GM12878-XiMat	blood
22	chr1:9813600-9824800	Weak transcription	Osteobl	bone
23	chr1:9813600-9825400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:9813600-9825800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:9813600-9831800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:9813600-9832400	Weak transcription	Right Ventricle	heart
27	chr1:9813800-9832400	Weak transcription	Adipose Nuclei	Adipose
28	chr1:9813800-9852200	Weak transcription	Right Atrium	heart
29	chr1:9814200-9827000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:9815400-9824000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:9815400-9824400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:9815400-9826000	Weak transcription	A549	lung
33	chr1:9815400-9829200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:9815400-9831600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:9815400-9832400	Weak transcription	Fetal Intestine Large	intestine
36	chr1:9815400-9832600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:9815600-9829600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:9815600-9830800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:9816200-9826200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:9816400-9824800	Weak transcription	NH-A	brain
41	chr1:9816400-9831800	Weak transcription	Brain Germinal Matrix	brain
42	chr1:9816600-9824400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:9816600-9842400	Weak transcription	HUVEC	blood vessel
44	chr1:9817800-9824600	Strong transcription	Dnd41	blood
45	chr1:9818600-9825000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:9819200-9825200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:9819600-9826800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:9820000-9826800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:9820000-9826800	Weak transcription	Brain Substantia Nigra	brain
50	chr1:9820200-9824600	Strong transcription	Fetal Stomach	stomach

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