Variant report

Variant	rs12047054
Chromosome Location	chr1:9814964-9814965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10779730	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10779731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10864435	0.83[CHD][hapmap]
rs10864436	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.81[EUR][1000 genomes]
rs10864437	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10864438	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11121484	0.83[CHD][hapmap];0.90[MEX][hapmap]
rs11121486	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs11121489	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11121490	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11121492	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs11121493	1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11674	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11804356	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11806520	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12021914	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12034239	0.81[EUR][1000 genomes]
rs12037599	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs12042293	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs12064975	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12075554	0.90[MEX][hapmap]
rs12078414	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12087051	0.84[EUR][1000 genomes]
rs12088273	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1220419	0.82[ASN][1000 genomes]
rs1228434	0.84[EUR][1000 genomes]
rs12568720	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12569008	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1615629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1631962	0.86[EUR][1000 genomes]
rs1660741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1660742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17034335	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap]
rs1767277	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs3934934	0.81[MEX][hapmap]
rs4512653	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4845975	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56109009	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57560942	0.88[EUR][1000 genomes]
rs59729812	0.88[EUR][1000 genomes]
rs6666296	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs6677664	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs6699320	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs72855716	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72855745	0.88[EUR][1000 genomes]
rs72855747	0.88[EUR][1000 genomes]
rs7526958	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7550246	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7550295	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs767762	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[EUR][1000 genomes]
rs935071	0.88[EUR][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9784000-9815400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:9784200-9815800	Strong transcription	Fetal Intestine Small	intestine
3	chr1:9786600-9815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:9787600-9815200	Strong transcription	Duodenum Mucosa	Duodenum
5	chr1:9789800-9815400	Strong transcription	Fetal Thymus	thymus
6	chr1:9789800-9815800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:9790600-9815400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:9791600-9816000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:9792000-9815600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:9793800-9815200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:9794000-9815600	Strong transcription	Fetal Stomach	stomach
12	chr1:9794200-9815600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:9794200-9815800	Strong transcription	Thymus	Thymus
14	chr1:9798200-9815600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:9798200-9816000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:9798600-9815400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:9798600-9815600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr1:9799400-9815600	Strong transcription	Dnd41	blood
19	chr1:9800000-9815200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:9800200-9815400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:9800600-9821600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:9801000-9815800	Weak transcription	Psoas Muscle	Psoas
23	chr1:9801200-9837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:9801400-9854200	Weak transcription	Fetal Kidney	kidney
25	chr1:9804400-9836600	Weak transcription	Small Intestine	intestine
26	chr1:9804600-9836600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:9804800-9815600	Weak transcription	HUVEC	blood vessel
28	chr1:9806000-9815600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:9806400-9815400	Strong transcription	Fetal Intestine Large	intestine
30	chr1:9806400-9825800	Weak transcription	HSMMtube	muscle
31	chr1:9806800-9819000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:9807600-9816200	Strong transcription	Primary T cells from cord blood	blood
33	chr1:9808000-9815000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:9808000-9815400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:9808000-9815400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:9808000-9815600	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:9808200-9815200	Strong transcription	Brain Hippocampus Middle	brain
38	chr1:9808200-9815400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:9808200-9815400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:9808200-9815400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:9808200-9815600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:9808400-9815800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:9810000-9815200	Weak transcription	Brain Substantia Nigra	brain
44	chr1:9810000-9815800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:9810000-9832400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:9810200-9816000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:9810200-9825800	Weak transcription	NHDF-Ad	bronchial
48	chr1:9810200-9826000	Weak transcription	Hela-S3	cervix
49	chr1:9810200-9826000	Weak transcription	HSMM	muscle
50	chr1:9810200-9829200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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