Variant report

Variant	rs6680771
Chromosome Location	chr1:113510952-113510953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113496701..113499764-chr1:113507961..113512647,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRIG2-4	chr1:113510657-113511609	ENSG00000226419
2	lnc-LRIG2-4	chr1:113510657-113511020	ENSG00000226419
3	lnc-LRIG2-3	chr1:113510657-113511080	NONHSAT005306

Variant related genes	Relation type
ENSG00000226419	Chromatin interaction
ENSG00000155380	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11102547	1.00[EUR][1000 genomes]
rs11102564	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11102570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11102572	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11102587	1.00[EUR][1000 genomes]
rs12058371	1.00[EUR][1000 genomes]
rs12061638	1.00[EUR][1000 genomes]
rs12061679	1.00[EUR][1000 genomes]
rs12063125	1.00[EUR][1000 genomes]
rs12063286	1.00[EUR][1000 genomes]
rs12063903	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12063907	1.00[EUR][1000 genomes]
rs12066276	1.00[EUR][1000 genomes]
rs12066409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12068534	1.00[EUR][1000 genomes]
rs12068812	1.00[EUR][1000 genomes]
rs12068820	1.00[EUR][1000 genomes]
rs12068935	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12069411	1.00[EUR][1000 genomes]
rs12069981	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075099	1.00[EUR][1000 genomes]
rs12075714	1.00[EUR][1000 genomes]
rs12078513	1.00[EUR][1000 genomes]
rs12079268	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079494	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079508	1.00[EUR][1000 genomes]
rs12079574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084281	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12090558	1.00[EUR][1000 genomes]
rs12093541	1.00[EUR][1000 genomes]
rs1216782	1.00[EUR][1000 genomes]
rs1216786	1.00[EUR][1000 genomes]
rs1216787	1.00[EUR][1000 genomes]
rs17030888	1.00[EUR][1000 genomes]
rs60953496	1.00[AMR][1000 genomes]
rs6657174	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6676854	1.00[EUR][1000 genomes]
rs6680949	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6699036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72996345	1.00[EUR][1000 genomes]
rs7511828	1.00[EUR][1000 genomes]
rs7513355	1.00[EUR][1000 genomes]
rs7518119	1.00[EUR][1000 genomes]
rs7530614	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7537295	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7540515	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7545283	1.00[EUR][1000 genomes]
rs7551138	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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	59 gene(s)	inside rSNPs	diseases
14	esv1827123	chr1:113496841-113531848	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers 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	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113499600-113525600	Weak transcription	Spleen	Spleen
2	chr1:113499800-113514800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:113500200-113524600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:113500200-113528600	Weak transcription	Lung	lung
5	chr1:113500200-113529000	Weak transcription	Esophagus	oesophagus
6	chr1:113500400-113520200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:113500600-113515000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:113500600-113535400	Weak transcription	Aorta	Aorta
9	chr1:113500800-113515400	Weak transcription	Fetal Kidney	kidney
10	chr1:113500800-113515800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:113501000-113525600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:113501600-113512800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:113501600-113512800	Weak transcription	Colonic Mucosa	Colon
14	chr1:113501600-113515600	Weak transcription	Thymus	Thymus
15	chr1:113501800-113511800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:113502000-113520600	Weak transcription	Fetal Brain Male	brain
17	chr1:113502400-113513600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:113502600-113511200	Strong transcription	Osteobl	bone
19	chr1:113502800-113511200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:113503000-113511200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:113503000-113511200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:113503000-113511200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:113503000-113511200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:113503000-113511800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:113503000-113515000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:113503000-113519600	Weak transcription	Brain Germinal Matrix	brain
27	chr1:113503200-113511200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:113503200-113511400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:113503200-113511400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr1:113503200-113511400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:113503200-113512200	Weak transcription	Small Intestine	intestine
32	chr1:113503400-113511600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:113503400-113515600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:113503600-113511200	Strong transcription	NHEK	skin
35	chr1:113503600-113525400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:113504800-113513600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:113504800-113516000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:113505800-113513200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:113506000-113511800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:113506000-113512200	Strong transcription	Dnd41	blood
41	chr1:113506600-113511800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:113506800-113511200	Strong transcription	K562	blood
43	chr1:113506800-113512200	Strong transcription	Fetal Stomach	stomach
44	chr1:113507000-113511200	Strong transcription	Primary T cells from cord blood	blood
45	chr1:113507000-113511200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:113507000-113511200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:113507000-113511200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:113507000-113511600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:113507000-113511800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:113507000-113512200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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