Variant report

Variant	rs12087408
Chromosome Location	chr1:9864113-9864114
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	chr1:9863213..9865031-chr1:9882665..9885379,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12059243	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12072320	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12083800	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12084163	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12092457	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094930	0.87[AMR][1000 genomes]
rs12096905	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12354258	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12354385	0.88[AFR][1000 genomes]
rs6658971	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6663532	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7514164	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9887930	0.83[AFR][1000 genomes]

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	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
5	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

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9843000-9864400	Weak transcription	Stomach Mucosa	stomach
2	chr1:9848600-9864600	Weak transcription	Small Intestine	intestine
3	chr1:9854000-9864600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:9854000-9871600	Weak transcription	Brain Germinal Matrix	brain
5	chr1:9854200-9865200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:9854400-9865200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:9855000-9864800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:9857200-9865000	Weak transcription	K562	blood
9	chr1:9857400-9864800	Weak transcription	Lung	lung
10	chr1:9857400-9865000	Weak transcription	HepG2	liver
11	chr1:9857400-9865200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:9857600-9867000	Weak transcription	Thymus	Thymus
13	chr1:9857600-9868600	Weak transcription	Spleen	Spleen
14	chr1:9857800-9867600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:9858600-9865000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:9858600-9865200	Weak transcription	Fetal Kidney	kidney
17	chr1:9858800-9864600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:9858800-9864600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:9858800-9865200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:9858800-9867000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:9859000-9867800	Weak transcription	Fetal Stomach	stomach
22	chr1:9859000-9870800	Weak transcription	Fetal Brain Female	brain
23	chr1:9859000-9871400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:9859000-9875000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:9859000-9881800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:9859000-9882400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:9859200-9864400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:9859200-9864400	Weak transcription	Pancreas	Pancrea
29	chr1:9859200-9864400	Weak transcription	HMEC	breast
30	chr1:9859200-9864600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:9859200-9864600	Weak transcription	Brain Anterior Caudate	brain
32	chr1:9859200-9864800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:9859200-9865000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:9859200-9867200	Weak transcription	Gastric	stomach
35	chr1:9859200-9867600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:9859200-9867600	Weak transcription	Brain Angular Gyrus	brain
37	chr1:9859200-9867600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:9859200-9868800	Weak transcription	Left Ventricle	heart
39	chr1:9859200-9868800	Weak transcription	Ovary	ovary
40	chr1:9859200-9868800	Weak transcription	Right Ventricle	heart
41	chr1:9859200-9869000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:9859200-9871000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:9859200-9871400	Weak transcription	A549	lung
44	chr1:9859200-9871800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:9859200-9874200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:9859200-9874800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:9859400-9864400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:9859400-9864400	Weak transcription	Fetal Thymus	thymus
49	chr1:9859400-9864600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr1:9859400-9864600	Weak transcription	Fetal Muscle Leg	muscle

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