Variant report

Variant	rs12128658
Chromosome Location	chr1:113639982-113639983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113629031..113632122-chr1:113632833..113640329,7	MCF-7	breast:
2	chr1:113639015..113640727-chr1:113641538..113644120,2	MCF-7	breast:
3	chr1:113639301..113642485-chr1:113643090..113645839,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198799	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11102584	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11102586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12031658	1.00[CHB][hapmap]
rs12071491	0.86[EUR][1000 genomes]
rs12117273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12118061	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12118532	1.00[EUR][1000 genomes]
rs12118642	1.00[AMR][1000 genomes]
rs12119387	0.83[EUR][1000 genomes]
rs12120401	0.83[EUR][1000 genomes]
rs12120441	0.83[EUR][1000 genomes]
rs12120738	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12123072	1.00[EUR][1000 genomes]
rs12123519	1.00[EUR][1000 genomes]
rs12123601	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12125675	0.83[EUR][1000 genomes]
rs12125708	0.83[EUR][1000 genomes]
rs12126304	0.83[EUR][1000 genomes]
rs12126316	1.00[AMR][1000 genomes]
rs12127415	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12129858	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12133057	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12136395	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12136941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12138968	1.00[AMR][1000 genomes]
rs12139726	0.83[EUR][1000 genomes]
rs12139899	0.83[EUR][1000 genomes]
rs12140067	0.86[EUR][1000 genomes]
rs12140651	1.00[AMR][1000 genomes]
rs12140676	1.00[AMR][1000 genomes]
rs12140810	0.83[EUR][1000 genomes]
rs12141018	1.00[AMR][1000 genomes]
rs12141415	1.00[EUR][1000 genomes]
rs12141540	0.83[EUR][1000 genomes]
rs12141541	0.83[EUR][1000 genomes]
rs12142449	0.83[EUR][1000 genomes]
rs12142475	0.83[EUR][1000 genomes]
rs12142510	0.83[EUR][1000 genomes]
rs12143171	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12143341	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12143430	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12145713	0.83[EUR][1000 genomes]
rs12145738	0.83[EUR][1000 genomes]
rs1216767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216793	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216802	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216805	1.00[ASN][1000 genomes]
rs1216807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216810	1.00[ASN][1000 genomes]
rs1216812	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184272	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12184320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12744661	1.00[EUR][1000 genomes]
rs1310142	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17031006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1728227	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1728229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1728240	0.86[EUR][1000 genomes]
rs1766864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1766865	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1778016	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778023	0.83[ASN][1000 genomes]
rs41296184	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41306207	1.00[AMR][1000 genomes]
rs4839291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6695183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74111210	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74111213	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518115	0.83[EUR][1000 genomes]
rs7531847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538813	0.86[EUR][1000 genomes]
rs7541246	0.83[EUR][1000 genomes]
rs7541520	0.83[EUR][1000 genomes]
rs7541703	0.83[EUR][1000 genomes]
rs7545814	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs946215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
7	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
8	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
9	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
10	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv437002	chr1:113592588-113658887	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr1:113617000-113645800	Weak transcription	Aorta	Aorta
2	chr1:113617200-113642600	Weak transcription	A549	lung
3	chr1:113622200-113645600	Weak transcription	Right Ventricle	heart
4	chr1:113622200-113645800	Weak transcription	Lung	lung
5	chr1:113625800-113646000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:113631800-113666600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:113633600-113672600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:113633800-113670000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:113633800-113672600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:113634200-113655200	Strong transcription	Hela-S3	cervix
11	chr1:113634200-113656000	Strong transcription	Dnd41	blood
12	chr1:113634200-113669800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:113634200-113669800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr1:113634200-113670000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:113634200-113671400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:113634200-113673000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:113634400-113655600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:113634400-113672600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:113634600-113644800	Strong transcription	Placenta	Placenta
20	chr1:113634600-113646800	Strong transcription	Primary hematopoietic stem cells	blood
21	chr1:113634600-113652200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:113634600-113655600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:113634600-113655600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:113634600-113666600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:113634600-113669800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:113634600-113669800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:113634600-113669800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:113634600-113670000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:113634600-113671200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:113634600-113671600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:113634600-113673000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:113634800-113644000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:113635000-113645800	Weak transcription	Stomach Mucosa	stomach
34	chr1:113635000-113666800	Strong transcription	Liver	Liver
35	chr1:113635000-113669600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:113635600-113652400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:113635800-113644800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:113635800-113649200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:113635800-113650600	Strong transcription	NH-A	brain
40	chr1:113635800-113655800	Strong transcription	Fetal Muscle Leg	muscle
41	chr1:113635800-113666600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:113635800-113669800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:113636000-113641800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:113636000-113644000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:113636000-113644600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:113636000-113644800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:113636000-113644800	Strong transcription	Colon Smooth Muscle	Colon
48	chr1:113636000-113644800	Strong transcription	Fetal Lung	lung
49	chr1:113636000-113647200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:113636000-113648600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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