Variant report

Variant	rs12094930
Chromosome Location	chr1:9854792-9854793
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9852615..9854985-chr1:9884936..9886688,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12059243	0.87[AMR][1000 genomes]
rs12068953	0.85[MKK][hapmap]
rs12072320	1.00[ASW][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs12083800	0.87[AMR][1000 genomes]
rs12084163	1.00[ASW][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs12087408	0.87[AMR][1000 genomes]
rs12092457	1.00[JPT][hapmap];0.87[MKK][hapmap];0.87[AMR][1000 genomes]
rs12096905	0.87[AMR][1000 genomes]
rs12354258	1.00[AMR][1000 genomes]
rs6658971	1.00[ASW][hapmap];0.83[LWK][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs6663532	0.87[AMR][1000 genomes]
rs7514164	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 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	nsv2298	chr1:9826286-9857487	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
7	esv1848817	chr1:9842576-9855529	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1821566	chr1:9842576-9856687	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv827475	chr1:9846555-9855119	Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv827586	chr1:9846555-9857371	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv498662	chr1:9846650-9856696	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv827697	chr1:9846837-9855347	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1815656	chr1:9847032-9856434	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1817934	chr1:9847032-9856434	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1818972	chr1:9847032-9856434	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv1823165	chr1:9847032-9856434	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv1823318	chr1:9847032-9856434	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1824497	chr1:9847032-9856434	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv1824898	chr1:9847032-9856434	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv1842948	chr1:9847032-9856434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv1843596	chr1:9847032-9856434	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	esv1846628	chr1:9847032-9856434	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	esv1851002	chr1:9847032-9856434	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv545378	chr1:9847032-9856434	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv1817417	chr1:9847032-9856687	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	esv1819093	chr1:9847032-9856826	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	esv1824318	chr1:9847032-9856826	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	esv1845506	chr1:9847032-9856826	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	esv1847729	chr1:9847032-9856826	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	esv1822763	chr1:9847032-9864493	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv545379	chr1:9847762-9856687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9811800-9857000	Weak transcription	Aorta	Aorta
2	chr1:9843000-9864400	Weak transcription	Stomach Mucosa	stomach
3	chr1:9843400-9858400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:9845800-9858200	Weak transcription	HMEC	breast
5	chr1:9847200-9858200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:9847400-9859800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:9848200-9857200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:9848200-9857200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:9848200-9860000	Weak transcription	Primary B cells from cord blood	blood
10	chr1:9848400-9854800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:9848400-9857200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:9848400-9858600	Weak transcription	Primary T cells from cord blood	blood
13	chr1:9848600-9856200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:9848600-9857200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:9848600-9864600	Weak transcription	Small Intestine	intestine
16	chr1:9849200-9858400	Weak transcription	Adipose Nuclei	Adipose
17	chr1:9849600-9856800	Weak transcription	Dnd41	blood
18	chr1:9851600-9854800	Enhancers	Fetal Muscle Leg	muscle
19	chr1:9852000-9855000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:9852000-9857000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:9852200-9854800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:9852200-9854800	Enhancers	Brain Cingulate Gyrus	brain
23	chr1:9852200-9854800	Enhancers	Brain Hippocampus Middle	brain
24	chr1:9852200-9854800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr1:9852200-9854800	Enhancers	Fetal Brain Male	brain
26	chr1:9852200-9854800	Enhancers	Pancreas	Pancrea
27	chr1:9852200-9855000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:9852200-9855000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr1:9852200-9855000	Enhancers	Brain Angular Gyrus	brain
30	chr1:9852200-9855000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:9852200-9855200	Enhancers	Fetal Heart	heart
32	chr1:9852400-9854800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:9852400-9856000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:9852600-9859000	Weak transcription	Placenta	Placenta
35	chr1:9852800-9854800	Weak transcription	HSMM	muscle
36	chr1:9852800-9855000	Weak transcription	Osteobl	bone
37	chr1:9852800-9855600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:9852800-9855600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:9852800-9856000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:9852800-9856800	Weak transcription	HepG2	liver
41	chr1:9852800-9857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:9852800-9857000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:9852800-9857200	Weak transcription	Fetal Stomach	stomach
44	chr1:9852800-9857800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:9852800-9858200	Weak transcription	Fetal Lung	lung
46	chr1:9853000-9854800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:9853000-9856800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:9853000-9856800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:9853000-9856800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:9853000-9857000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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