Variant report

Variant	rs61832743
Chromosome Location	chr10:5741462-5741463
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5706900..5709374-chr10:5740250..5741979,2	MCF-7	breast:
2	chr10:5724274..5728540-chr10:5734829..5741563,8	MCF-7	breast:
3	chr10:5726410..5728417-chr10:5738015..5741917,3	MCF-7	breast:
4	chr10:5734758..5736346-chr10:5739333..5741720,2	MCF-7	breast:
5	chr10:5739796..5741781-chr10:5749171..5751664,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALML3-1	chr10:5741411-5741700	NONHSAT011177

Variant related genes	Relation type
ENSG00000108021	Chromatin interaction
ENSG00000196372	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10737012	0.81[EUR][1000 genomes]
rs10795510	0.81[EUR][1000 genomes]
rs11254266	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282457	0.85[ASN][1000 genomes]
rs45575338	0.81[AFR][1000 genomes]
rs4748307	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4748572	0.81[AFR][1000 genomes]
rs4750553	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55913768	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61832744	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7078711	0.81[EUR][1000 genomes]
rs7096742	0.80[EUR][1000 genomes]
rs72774056	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72774070	0.81[AFR][1000 genomes]
rs72774075	0.81[AFR][1000 genomes]
rs72774077	0.81[AFR][1000 genomes]
rs72774078	0.81[AFR][1000 genomes]
rs7909988	0.80[EUR][1000 genomes]
rs7910414	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv1796213	chr10:5716555-5766165	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv522415	chr10:5721653-5768493	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
7	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1050663	chr10:5737979-5785918	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv528504	chr10:5739054-5754611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61832743	GDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5728800-5746800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr10:5734800-5763400	Weak transcription	HSMM	muscle
3	chr10:5735200-5743000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:5735200-5749000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr10:5735200-5750600	Weak transcription	Gastric	stomach
6	chr10:5735200-5767000	Weak transcription	Fetal Muscle Leg	muscle
7	chr10:5735400-5744800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:5735400-5750800	Weak transcription	Spleen	Spleen
9	chr10:5735400-5761600	Weak transcription	NHEK	skin
10	chr10:5735400-5762000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:5735800-5741800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr10:5735800-5752800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr10:5736200-5742600	Weak transcription	Brain Angular Gyrus	brain
14	chr10:5736200-5751600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:5736400-5753000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:5736600-5741600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr10:5736800-5742000	Weak transcription	Primary T cells from cord blood	blood
18	chr10:5736800-5742000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:5737000-5742000	Weak transcription	Brain Substantia Nigra	brain
20	chr10:5737000-5742600	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:5737000-5743600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr10:5737400-5744200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr10:5737400-5744800	Weak transcription	Liver	Liver
24	chr10:5737600-5744200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr10:5738200-5745200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr10:5738400-5744200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr10:5738600-5752400	Weak transcription	Primary B cells from cord blood	blood
28	chr10:5738600-5752800	Weak transcription	Right Atrium	heart
29	chr10:5738600-5769000	Weak transcription	Left Ventricle	heart
30	chr10:5739400-5741600	Enhancers	Primary B cells from peripheral blood	blood
31	chr10:5739400-5745000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr10:5739600-5752800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr10:5740200-5742000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr10:5740200-5742400	Weak transcription	HepG2	liver
35	chr10:5740200-5752000	Weak transcription	Stomach Mucosa	stomach
36	chr10:5740200-5752800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr10:5740400-5742200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr10:5740400-5742800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr10:5740400-5768600	Weak transcription	Psoas Muscle	Psoas
40	chr10:5740600-5742000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr10:5740600-5742400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr10:5740600-5742400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr10:5740600-5742400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr10:5740800-5742200	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr10:5740800-5743600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr10:5740800-5744800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr10:5741000-5741600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:5741000-5742200	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr10:5741000-5743200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:5741200-5741600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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