Variant report

Variant	rs1778210
Chromosome Location	chr1:95058106-95058107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95054539..95057690-chr1:95058025..95060713,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-F3-3	chr1:95058100-95058233	l_89_chr1:94917575-94970548_76bGuttman_hLF

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10399782	1.00[EUR][1000 genomes]
rs1146475	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146478	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146479	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146486	0.84[AFR][1000 genomes]
rs1146499	0.83[AFR][1000 genomes]
rs1146503	0.82[AFR][1000 genomes]
rs1146504	0.84[AFR][1000 genomes]
rs1146506	1.00[EUR][1000 genomes]
rs1146508	0.84[AFR][1000 genomes]
rs1146516	1.00[EUR][1000 genomes]
rs12064943	1.00[EUR][1000 genomes]
rs12065028	1.00[EUR][1000 genomes]
rs1303133	0.84[AFR][1000 genomes]
rs1303136	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1343483	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1577920	1.00[EUR][1000 genomes]
rs1617719	1.00[EUR][1000 genomes]
rs1687938	1.00[EUR][1000 genomes]
rs1687939	1.00[EUR][1000 genomes]
rs1687942	1.00[EUR][1000 genomes]
rs1687945	1.00[EUR][1000 genomes]
rs1687969	1.00[EUR][1000 genomes]
rs17112279	1.00[EUR][1000 genomes]
rs1747648	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1747656	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1747658	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1749540	1.00[EUR][1000 genomes]
rs1765625	1.00[EUR][1000 genomes]
rs1765631	1.00[EUR][1000 genomes]
rs1765633	1.00[EUR][1000 genomes]
rs1765634	1.00[EUR][1000 genomes]
rs1765653	1.00[EUR][1000 genomes]
rs1772902	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1778224	0.84[AFR][1000 genomes]
rs2094824	1.00[EUR][1000 genomes]
rs2798944	1.00[EUR][1000 genomes]
rs2971948	1.00[EUR][1000 genomes]
rs479627	1.00[EUR][1000 genomes]
rs484420	1.00[EUR][1000 genomes]
rs4847315	1.00[EUR][1000 genomes]
rs512648	1.00[EUR][1000 genomes]
rs513976	1.00[EUR][1000 genomes]
rs529642	1.00[EUR][1000 genomes]
rs598962	1.00[EUR][1000 genomes]
rs610088	1.00[EUR][1000 genomes]
rs630382	1.00[EUR][1000 genomes]
rs6660037	1.00[EUR][1000 genomes]
rs698945	1.00[EUR][1000 genomes]
rs768967	1.00[EUR][1000 genomes]
rs860909	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv871279	chr1:95028981-95083836	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1804937	chr1:95051930-95081587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95046000-95065400	Weak transcription	Fetal Intestine Large	intestine
2	chr1:95055000-95059200	Enhancers	Brain Cingulate Gyrus	brain
3	chr1:95055000-95061400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:95055000-95061600	Enhancers	Brain Anterior Caudate	brain
5	chr1:95055000-95062000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:95055200-95059200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:95055400-95061800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:95055800-95058200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:95056000-95059000	Weak transcription	Placenta	Placenta
10	chr1:95056200-95058200	Weak transcription	Stomach Mucosa	stomach
11	chr1:95056200-95067800	Weak transcription	Gastric	stomach
12	chr1:95056400-95060200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:95056400-95060600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:95056400-95061000	Weak transcription	Fetal Intestine Small	intestine
15	chr1:95056400-95061400	Weak transcription	Fetal Lung	lung
16	chr1:95056600-95058400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:95056600-95058600	Weak transcription	Fetal Stomach	stomach
18	chr1:95056600-95060000	Weak transcription	Hela-S3	cervix
19	chr1:95056600-95060600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:95056600-95060600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:95056600-95060800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:95056600-95060800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:95056800-95059200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:95056800-95059600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:95056800-95061000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:95056800-95061200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:95056800-95061200	Weak transcription	NHLF	lung
28	chr1:95056800-95069000	Weak transcription	Right Atrium	heart
29	chr1:95057000-95060600	Enhancers	Brain Substantia Nigra	brain
30	chr1:95057000-95061600	Enhancers	Brain Hippocampus Middle	brain
31	chr1:95057200-95061000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:95057400-95069000	Weak transcription	Aorta	Aorta
33	chr1:95057600-95058200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:95057600-95058600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:95057600-95059200	Enhancers	Brain Germinal Matrix	brain
36	chr1:95057800-95058200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:95057800-95058400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:95057800-95061400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:95058000-95058200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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