Variant report

Variant	rs3750039
Chromosome Location	chr7:6370305-6370306
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAC1-2	chr7:6370213-6370871	NONHSAT118994

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10951979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3750040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6952125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6965687	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription 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 target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv482829	chr7:6231809-6407606	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1032987	chr7:6246313-6373054	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv538714	chr7:6246313-6373054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv1020251	chr7:6309528-6379941	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1025381	chr7:6356704-6409818	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv538716	chr7:6365534-6400845	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6357800-6386200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:6358000-6371600	Weak transcription	HMEC	breast
3	chr7:6358000-6372200	Weak transcription	NHDF-Ad	bronchial
4	chr7:6358000-6378400	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:6358000-6386000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:6358200-6372200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:6358200-6372400	Weak transcription	Right Atrium	heart
8	chr7:6358200-6387200	Weak transcription	HepG2	liver
9	chr7:6358200-6387600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:6358200-6387600	Weak transcription	HSMM	muscle
11	chr7:6358200-6387600	Weak transcription	NH-A	brain
12	chr7:6362800-6387800	Weak transcription	Fetal Lung	lung
13	chr7:6363000-6378000	Weak transcription	Colon Smooth Muscle	Colon
14	chr7:6363000-6385800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:6363000-6386200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:6363000-6387600	Weak transcription	NHEK	skin
17	chr7:6363200-6378400	Weak transcription	Dnd41	blood
18	chr7:6363200-6386200	Weak transcription	Fetal Brain Male	brain
19	chr7:6366000-6371800	Weak transcription	Aorta	Aorta
20	chr7:6366200-6370400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr7:6367400-6386400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:6367600-6371600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:6367800-6378200	Weak transcription	Brain Angular Gyrus	brain
24	chr7:6368200-6370400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:6368400-6387800	Weak transcription	Colonic Mucosa	Colon
26	chr7:6368800-6370800	Strong transcription	Fetal Brain Female	brain
27	chr7:6368800-6372000	Strong transcription	Primary T cells from cord blood	blood
28	chr7:6368800-6372000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:6368800-6380000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:6368800-6387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:6369200-6370600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:6369200-6370800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr7:6369200-6370800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:6369200-6370800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr7:6369200-6371200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:6369200-6382200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr7:6369400-6370400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr7:6369400-6370600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr7:6369400-6370600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr7:6369400-6370600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr7:6369400-6370600	Strong transcription	Brain Anterior Caudate	brain
42	chr7:6369400-6370600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:6369400-6370800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:6369400-6370800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr7:6369400-6370800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:6369400-6370800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:6369400-6370800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:6369400-6370800	Strong transcription	Liver	Liver
49	chr7:6369400-6370800	Strong transcription	Brain Germinal Matrix	brain
50	chr7:6369400-6370800	Strong transcription	Duodenum Mucosa	Duodenum

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