Variant report

Variant	rs7550246
Chromosome Location	chr1:9808302-9808303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10779730	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10779731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs10864437	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864438	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121484	0.83[CHD][hapmap];0.85[MEX][hapmap]
rs11121486	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs11121489	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11121490	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11121492	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs11121493	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11674	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804356	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11806520	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12021914	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12034239	0.86[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]
rs12047054	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]
rs12064975	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12075554	0.85[MEX][hapmap]
rs12078414	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs12087051	0.89[EUR][1000 genomes]
rs12088273	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1220419	0.80[ASN][1000 genomes]
rs1228434	0.89[EUR][1000 genomes]
rs12568720	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12569008	0.88[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1615629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1631962	0.87[EUR][1000 genomes]
rs1660741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1660742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17034335	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs17034340	0.82[EUR][1000 genomes]
rs1767277	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs2788605	0.84[EUR][1000 genomes]
rs4512653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4585981	0.84[EUR][1000 genomes]
rs4845975	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56109009	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57560942	0.89[EUR][1000 genomes]
rs59729812	0.89[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];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs72855716	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72855733	0.82[EUR][1000 genomes]
rs72855735	0.84[EUR][1000 genomes]
rs72855745	0.89[EUR][1000 genomes]
rs72855747	0.89[EUR][1000 genomes]
rs7526958	0.88[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[YRI][hapmap];0.82[AMR][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[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs935071	0.89[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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9750600-9813000	Weak transcription	Right Atrium	heart
2	chr1:9781200-9813200	Strong transcription	Stomach Smooth Muscle	stomach
3	chr1:9784000-9815400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:9784200-9815800	Strong transcription	Fetal Intestine Small	intestine
5	chr1:9786400-9814000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:9786600-9815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:9786800-9814000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:9787000-9813000	Weak transcription	Fetal Heart	heart
9	chr1:9787400-9811800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:9787600-9812000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:9787600-9813200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:9787600-9815200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr1:9788400-9811800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:9789800-9815400	Strong transcription	Fetal Thymus	thymus
15	chr1:9789800-9815800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:9790600-9815400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:9791600-9814200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:9791600-9816000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:9792000-9815600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:9792600-9811000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:9793000-9810000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:9793000-9811800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:9793400-9813200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:9793800-9815200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:9794000-9815600	Strong transcription	Fetal Stomach	stomach
26	chr1:9794200-9815600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:9794200-9815800	Strong transcription	Thymus	Thymus
28	chr1:9794800-9809600	Weak transcription	NHDF-Ad	bronchial
29	chr1:9797600-9814400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:9798200-9815600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:9798200-9816000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:9798600-9815400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:9798600-9815600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:9799400-9815600	Strong transcription	Dnd41	blood
35	chr1:9800000-9815200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:9800200-9815400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:9800400-9813400	Strong transcription	Colonic Mucosa	Colon
38	chr1:9800600-9821600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:9801000-9815800	Weak transcription	Psoas Muscle	Psoas
40	chr1:9801200-9837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:9801400-9811400	Weak transcription	Fetal Brain Male	brain
42	chr1:9801400-9854200	Weak transcription	Fetal Kidney	kidney
43	chr1:9801600-9813000	Weak transcription	K562	blood
44	chr1:9802600-9809400	Weak transcription	Hela-S3	cervix
45	chr1:9802600-9809400	Weak transcription	HSMM	muscle
46	chr1:9804400-9808600	Weak transcription	NH-A	brain
47	chr1:9804400-9813000	Weak transcription	A549	lung
48	chr1:9804400-9836600	Weak transcription	Small Intestine	intestine
49	chr1:9804600-9808800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:9804600-9809200	Weak transcription	Placenta Amnion	Placenta Amnion

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