Variant report

Variant	rs12603380
Chromosome Location	chr17:46204408-46204409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46202062..46204690-chr17:46205157..46208075,2	K562	blood:
2	chr17:46194453..46197293-chr17:46201950..46204423,2	MCF-7	breast:
3	chr17:46101392..46102971-chr17:46203162..46205117,2	MCF-7	breast:
4	chr17:46202789..46205247-chr17:46215518..46217432,2	K562	blood:
5	chr17:46107614..46109746-chr17:46202771..46206014,3	K562	blood:
6	chr17:46175748..46179895-chr17:46202616..46205569,5	MCF-7	breast:
7	chr17:46174713..46176905-chr17:46204166..46206499,2	MCF-7	breast:
8	chr17:46183681..46186136-chr17:46203632..46206520,3	MCF-7	breast:
9	chr17:46103475..46106134-chr17:46203314..46206264,3	MCF-7	breast:
10	chr17:46101075..46105793-chr17:46203518..46208640,6	MCF-7	breast:
11	chr17:46202911..46205247-chr17:46215503..46217018,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX11-6	chr17:46204111-46206694	NONHSAT054385

No data

Variant related genes	Relation type
ENSG00000002919	Chromatin interaction
ENSG00000108468	Chromatin interaction
ENSG00000005243	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1002330	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10445339	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10445377	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10853098	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11870056	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12603115	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12941830	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12947089	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12950225	0.82[EUR][1000 genomes]
rs12952670	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1316657	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17681336	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1860862	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1860863	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2021752	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2021811	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2041572	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2072441	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2109982	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2123341	0.86[AMR][1000 genomes]
rs2278868	0.81[AMR][1000 genomes]
rs2305433	0.86[AMR][1000 genomes]
rs2924257	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34949267	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3792692	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3792694	0.81[AMR][1000 genomes]
rs3805363	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3805370	0.81[AMR][1000 genomes]
rs3805371	0.81[AMR][1000 genomes]
rs3897986	0.86[AMR][1000 genomes]
rs3944039	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62064954	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7220768	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7220922	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7223867	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7225435	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7225550	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7225865	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs758999	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8069263	0.83[AMR][1000 genomes]
rs8071267	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs882380	0.83[AMR][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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46188200-46207400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:46190000-46204800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr17:46190400-46205000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr17:46191200-46220800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:46191600-46204600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:46191800-46204600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46192400-46204800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:46192400-46205400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr17:46192800-46205600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr17:46194400-46204600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr17:46194800-46205000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr17:46196800-46204800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:46196800-46208800	Weak transcription	K562	blood
14	chr17:46197800-46221000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:46198400-46204800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr17:46199400-46212400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:46199800-46209600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr17:46200000-46204800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr17:46200200-46204800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr17:46200200-46205000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr17:46200200-46206000	Weak transcription	Pancreas	Pancrea
22	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr17:46200600-46205800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr17:46200600-46206400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr17:46200600-46209000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr17:46200600-46209600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr17:46200800-46204600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:46200800-46204800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr17:46200800-46204800	Weak transcription	NHDF-Ad	bronchial
30	chr17:46200800-46204800	Weak transcription	NHLF	lung
31	chr17:46200800-46207400	Weak transcription	Right Ventricle	heart
32	chr17:46200800-46208400	Weak transcription	Colon Smooth Muscle	Colon
33	chr17:46200800-46209000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr17:46200800-46212400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:46201000-46204600	Weak transcription	Aorta	Aorta
36	chr17:46201000-46205400	Weak transcription	Fetal Lung	lung
37	chr17:46201000-46205400	Weak transcription	Left Ventricle	heart
38	chr17:46201000-46206400	Weak transcription	Ovary	ovary
39	chr17:46201000-46206600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr17:46201000-46207600	Weak transcription	Dnd41	blood
41	chr17:46201200-46204800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:46201200-46205600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr17:46201200-46206000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:46201200-46207000	Weak transcription	Fetal Intestine Large	intestine
45	chr17:46201200-46208000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:46201200-46209600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr17:46201400-46204600	Weak transcription	NH-A	brain
48	chr17:46201400-46204800	Weak transcription	Brain Substantia Nigra	brain
49	chr17:46201400-46205200	Weak transcription	Brain Anterior Caudate	brain
50	chr17:46201400-46205200	Weak transcription	Brain Inferior Temporal Lobe	brain

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