Variant report

Variant	rs2996295
Chromosome Location	chr1:113424469-113424470
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113423272..113424581-chr1:113497804..113499381,4	K562	blood:
2	chr1:113422315..113424969-chr1:113580165..113583110,2	K562	blood:
3	chr1:113421698..113424854-chr1:113496536..113501677,6	K562	blood:
4	chr1:113421698..113424521-chr1:113497162..113501677,6	K562	blood:
5	chr1:113424350..113426244-chr1:113426854..113428692,2	MCF-7	breast:
6	chr1:113392230..113394904-chr1:113422287..113425247,2	MCF-7	breast:
7	chr1:113422181..113424521-chr1:113435432..113438293,2	K562	blood:
8	chr1:113423539..113425457-chr1:113613953..113617483,4	K562	blood:
9	chr1:113423643..113425440-chr1:113613953..113616307,2	K562	blood:
10	chr1:113421587..113424736-chr1:113583992..113587746,3	K562	blood:
11	chr1:113423151..113424795-chr1:113615741..113617336,2	MCF-7	breast:
12	chr1:113423270..113424538-chr1:113584948..113585944,13	K562	blood:
13	chr1:113424435..113426998-chr1:113430244..113432680,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226419	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000198799	Chromatin interaction
ENSG00000238198	Chromatin interaction
ENSG00000224167	Chromatin interaction
ENSG00000215866	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10399593	0.95[ASN][1000 genomes]
rs1049434	0.87[ASW][hapmap]
rs10857979	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10857980	0.83[CEU][hapmap];0.82[GIH][hapmap]
rs11102559	0.95[ASN][1000 genomes]
rs12025191	0.94[ASN][1000 genomes]
rs1216538	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1539624	0.88[CHD][hapmap]
rs1539625	0.80[CHD][hapmap]
rs2002402	0.94[ASN][1000 genomes]
rs2360009	0.96[ASN][1000 genomes]
rs2884871	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789592	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs57549167	0.91[ASN][1000 genomes]
rs61819971	0.92[ASN][1000 genomes]
rs61819997	0.93[ASN][1000 genomes]
rs6537765	0.87[ASW][hapmap];0.87[MEX][hapmap]
rs6670224	0.84[CEU][hapmap]
rs6670866	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169	0.87[ASW][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv818378	chr1:113263711-113434818	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1008434	chr1:113288282-113447426	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	esv3362439	chr1:113376621-113450321	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2996295	LRIG2	cis	cerebellum	SCAN
rs2996295	GNAI3	cis	cerebellum	SCAN
rs2996295	OVGP1	cis	cerebellum	SCAN
rs2996295	DENND2C	cis	cerebellum	SCAN
rs2996295	AMPD1	cis	parietal	SCAN
rs2996295	DENND2C	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113415000-113424600	Weak transcription	Right Atrium	heart
2	chr1:113416000-113424600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:113421200-113424600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:113421400-113424600	Weak transcription	Fetal Brain Female	brain
5	chr1:113421400-113424800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:113421400-113435200	Weak transcription	Fetal Heart	heart
7	chr1:113421600-113424600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:113422000-113425800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:113423200-113424600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:113423200-113424600	Enhancers	Stomach Mucosa	stomach
11	chr1:113423400-113425200	Enhancers	Brain Substantia Nigra	brain
12	chr1:113423400-113425400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:113423400-113425400	Enhancers	Brain Hippocampus Middle	brain
14	chr1:113423400-113425600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:113423400-113425600	Enhancers	NHEK	skin
16	chr1:113423400-113425800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:113423600-113424600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:113423600-113424800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:113423600-113425200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:113423600-113425400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:113423600-113425400	Enhancers	HMEC	breast
22	chr1:113423600-113425400	Enhancers	K562	blood
23	chr1:113423600-113425600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:113423600-113425600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:113423600-113425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:113423600-113425800	Enhancers	HSMM	muscle
27	chr1:113423600-113426000	Enhancers	Fetal Muscle Leg	muscle
28	chr1:113423600-113426200	Enhancers	Placenta	Placenta
29	chr1:113423800-113424600	Weak transcription	Esophagus	oesophagus
30	chr1:113423800-113424600	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr1:113423800-113425200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:113423800-113425600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:113423800-113425800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr1:113423800-113425800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:113423800-113425800	Enhancers	Adipose Nuclei	Adipose
36	chr1:113423800-113425800	Enhancers	Duodenum Mucosa	Duodenum
37	chr1:113423800-113426600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr1:113424000-113424600	Enhancers	Osteobl	bone
39	chr1:113424000-113425600	Enhancers	Colonic Mucosa	Colon
40	chr1:113424200-113424600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:113424200-113425600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:113424200-113425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:113424200-113425800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr1:113424400-113424600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:113424400-113424600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:113424400-113424800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr1:113424400-113425000	Enhancers	Brain Anterior Caudate	brain
48	chr1:113424400-113425000	Enhancers	Fetal Intestine Large	intestine
49	chr1:113424400-113425200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:113424400-113425200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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