Variant report

Variant	rs2234416
Chromosome Location	chr13:30346188-30346189
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30344923..30346437-chr13:30688756..30689754,7	MCF-7	breast:
2	chr13:30342827..30348055-chr13:30683488..30688791,7	MCF-7	breast:
3	chr13:30344222..30347052-chr13:30686907..30688799,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1058650	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11147398	0.83[ASN][1000 genomes]
rs12872400	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1323931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1410110	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1854176	0.87[ASN][1000 genomes]
rs1927193	0.86[ASN][1000 genomes]
rs2025604	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2182129	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2388246	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2388247	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.82[ASN][1000 genomes]
rs2761938	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs278049	0.82[CHB][hapmap]
rs35541102	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4083610	0.83[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4238128	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4265673	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4297554	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4387451	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4769772	0.88[ASN][1000 genomes]
rs4769775	0.83[ASN][1000 genomes]
rs6490429	0.82[ASN][1000 genomes]
rs6490430	0.82[ASN][1000 genomes]
rs72623487	0.95[ASN][1000 genomes]
rs7320474	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7326253	0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7330356	0.82[CHB][hapmap]
rs7335148	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7342470	0.85[ASN][1000 genomes]
rs765404	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7981622	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7995666	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9314972	0.86[ASN][1000 genomes]
rs9314973	0.86[ASN][1000 genomes]
rs9314974	0.86[ASN][1000 genomes]
rs9314975	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9314978	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9506226	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9506229	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9506231	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9506233	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9508550	0.87[ASN][1000 genomes]
rs9508553	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9508554	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9508557	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9508558	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9508559	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9508560	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9508561	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9508564	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9550494	0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9551739	0.88[ASN][1000 genomes]
rs9551741	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9551744	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9551751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9551753	0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9578136	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578139	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30328800-30347800	Weak transcription	Fetal Kidney	kidney
2	chr13:30328800-30351800	Weak transcription	NH-A	brain
3	chr13:30328800-30352600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr13:30329200-30351200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr13:30330600-30355000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:30333200-30353800	Weak transcription	Gastric	stomach
7	chr13:30333200-30360200	Weak transcription	Pancreas	Pancrea
8	chr13:30333200-30368200	Weak transcription	Aorta	Aorta
9	chr13:30333400-30357000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr13:30335200-30356800	Weak transcription	GM12878-XiMat	blood
12	chr13:30335400-30349800	Weak transcription	Fetal Stomach	stomach
13	chr13:30336400-30357000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:30336600-30353800	Weak transcription	Psoas Muscle	Psoas
15	chr13:30337600-30363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:30337800-30359800	Weak transcription	HMEC	breast
17	chr13:30338400-30354000	Weak transcription	Colon Smooth Muscle	Colon
18	chr13:30338400-30360000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr13:30338400-30360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr13:30338600-30357000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr13:30338800-30347400	Weak transcription	Stomach Mucosa	stomach
22	chr13:30339000-30360200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr13:30339000-30364200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr13:30339400-30350800	Weak transcription	Hela-S3	cervix
25	chr13:30339600-30349600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr13:30339800-30346400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr13:30341000-30347400	Weak transcription	Brain Substantia Nigra	brain
28	chr13:30341200-30346600	Weak transcription	NHLF	lung
29	chr13:30341200-30373200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:30341400-30347800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr13:30341400-30348600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:30341400-30348600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr13:30341400-30349600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:30341400-30352200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr13:30341400-30360200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr13:30341600-30347200	Weak transcription	HUVEC	blood vessel
37	chr13:30341600-30349800	Weak transcription	Fetal Lung	lung
38	chr13:30341600-30353000	Weak transcription	Fetal Intestine Large	intestine
39	chr13:30341600-30356800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr13:30341600-30357200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr13:30341600-30360200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:30341800-30346400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr13:30341800-30347000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr13:30341800-30347200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr13:30341800-30347800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr13:30341800-30347800	Weak transcription	Thymus	Thymus
47	chr13:30341800-30349000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr13:30341800-30350600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr13:30341800-30351000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr13:30341800-30353800	Weak transcription	Primary B cells from peripheral blood	blood

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