Variant report

Variant	rs841688
Chromosome Location	chr1:95059032-95059033
allele	A/T
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:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1098724	0.96[ASN][1000 genomes]
rs1098726	0.97[ASN][1000 genomes]
rs11165173	0.90[JPT][hapmap]
rs12406950	0.82[ASN][1000 genomes]
rs12408608	0.94[ASN][1000 genomes]
rs1772895	0.94[ASN][1000 genomes]
rs2798940	0.96[ASN][1000 genomes]
rs34248730	1.00[ASN][1000 genomes]
rs7542900	0.94[ASN][1000 genomes]
rs841684	0.94[ASN][1000 genomes]
rs841685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs841687	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs841689	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs841690	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs841705	1.00[ASN][1000 genomes]
rs841708	0.96[ASN][1000 genomes]
rs866365	0.96[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs841688	HFM1	cis	cerebellum	SCAN

Chromatin state (count:42 , 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	chr1:95056200-95067800	Weak transcription	Gastric	stomach
9	chr1:95056400-95060200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:95056400-95060600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:95056400-95061000	Weak transcription	Fetal Intestine Small	intestine
12	chr1:95056400-95061400	Weak transcription	Fetal Lung	lung
13	chr1:95056600-95060000	Weak transcription	Hela-S3	cervix
14	chr1:95056600-95060600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:95056600-95060600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:95056600-95060800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:95056600-95060800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr1:95056800-95059200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:95056800-95059600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:95056800-95061000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:95056800-95061200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:95056800-95061200	Weak transcription	NHLF	lung
23	chr1:95056800-95069000	Weak transcription	Right Atrium	heart
24	chr1:95057000-95060600	Enhancers	Brain Substantia Nigra	brain
25	chr1:95057000-95061600	Enhancers	Brain Hippocampus Middle	brain
26	chr1:95057200-95061000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:95057400-95069000	Weak transcription	Aorta	Aorta
28	chr1:95057600-95059200	Enhancers	Brain Germinal Matrix	brain
29	chr1:95057800-95061400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:95058200-95059400	Enhancers	Stomach Mucosa	stomach
31	chr1:95058200-95060800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:95058400-95059200	Enhancers	Brain Angular Gyrus	brain
33	chr1:95058400-95059600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:95058600-95059200	Enhancers	Fetal Stomach	stomach
35	chr1:95058600-95060000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:95058800-95059200	Enhancers	Fetal Brain Male	brain
37	chr1:95059000-95059200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr1:95059000-95059200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:95059000-95059600	Enhancers	Fetal Muscle Trunk	muscle
40	chr1:95059000-95060000	Enhancers	Placenta	Placenta
41	chr1:95059000-95060600	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:95059000-95061400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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