Variant report

Variant	rs11121493
Chromosome Location	chr1:9864493-9864494
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	chr1:9864446..9867087-chr1:9902176..9904025,2	MCF-7	breast:
2	chr1:9863213..9865031-chr1:9882665..9885379,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10779731	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10864435	0.82[CHD][hapmap];0.83[MEX][hapmap]
rs10864436	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs10864437	0.87[EUR][1000 genomes]
rs10864438	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11121484	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs11121486	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap]
rs11121490	0.83[EUR][1000 genomes]
rs11121492	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11674	0.89[EUR][1000 genomes]
rs11806520	0.93[EUR][1000 genomes]
rs12034239	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12037599	0.85[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap]
rs12042293	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap]
rs12047054	1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs12078414	1.00[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs12087051	0.85[EUR][1000 genomes]
rs12088273	0.87[EUR][1000 genomes]
rs1220419	0.89[AMR][1000 genomes]
rs1228434	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12568720	0.85[CEU][hapmap]
rs12569008	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs1615629	1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1631962	0.84[EUR][1000 genomes]
rs1660741	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1660742	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17034335	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17034340	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1767277	1.00[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2788605	0.94[EUR][1000 genomes]
rs4585981	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56109009	0.89[EUR][1000 genomes]
rs57480158	0.86[EUR][1000 genomes]
rs57560942	0.85[EUR][1000 genomes]
rs59729812	0.85[EUR][1000 genomes]
rs6699320	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs72855716	0.89[EUR][1000 genomes]
rs72855733	0.92[EUR][1000 genomes]
rs72855735	0.94[EUR][1000 genomes]
rs72855745	0.85[EUR][1000 genomes]
rs72855747	0.85[EUR][1000 genomes]
rs7526958	0.85[CEU][hapmap]
rs7550246	0.89[EUR][1000 genomes]
rs7550295	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs767762	1.00[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs935071	0.85[EUR][1000 genomes]
rs946277	0.86[EUR][1000 genomes]
rs946278	0.86[EUR][1000 genomes]
rs946279	0.86[EUR][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:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9848600-9864600	Weak transcription	Small Intestine	intestine
2	chr1:9854000-9864600	Weak transcription	Fetal Intestine Small	intestine
3	chr1:9854000-9871600	Weak transcription	Brain Germinal Matrix	brain
4	chr1:9854200-9865200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:9854400-9865200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:9855000-9864800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:9857200-9865000	Weak transcription	K562	blood
8	chr1:9857400-9864800	Weak transcription	Lung	lung
9	chr1:9857400-9865000	Weak transcription	HepG2	liver
10	chr1:9857400-9865200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:9857600-9867000	Weak transcription	Thymus	Thymus
12	chr1:9857600-9868600	Weak transcription	Spleen	Spleen
13	chr1:9857800-9867600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:9858600-9865000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:9858600-9865200	Weak transcription	Fetal Kidney	kidney
16	chr1:9858800-9864600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:9858800-9864600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:9858800-9865200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:9858800-9867000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:9859000-9867800	Weak transcription	Fetal Stomach	stomach
21	chr1:9859000-9870800	Weak transcription	Fetal Brain Female	brain
22	chr1:9859000-9871400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:9859000-9875000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:9859000-9881800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:9859000-9882400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:9859200-9864600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:9859200-9864600	Weak transcription	Brain Anterior Caudate	brain
28	chr1:9859200-9864800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:9859200-9865000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:9859200-9867200	Weak transcription	Gastric	stomach
31	chr1:9859200-9867600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:9859200-9867600	Weak transcription	Brain Angular Gyrus	brain
33	chr1:9859200-9867600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr1:9859200-9868800	Weak transcription	Left Ventricle	heart
35	chr1:9859200-9868800	Weak transcription	Ovary	ovary
36	chr1:9859200-9868800	Weak transcription	Right Ventricle	heart
37	chr1:9859200-9869000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:9859200-9871000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:9859200-9871400	Weak transcription	A549	lung
40	chr1:9859200-9871800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:9859200-9874200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:9859200-9874800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:9859400-9864600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:9859400-9864600	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:9859400-9864600	Weak transcription	Placenta	Placenta
46	chr1:9859400-9869600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:9859400-9881600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:9860000-9865000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:9860400-9865200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:9860400-9867600	Weak transcription	Primary hematopoietic stem cells	blood

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