Variant report

Variant	rs6667621
Chromosome Location	chr1:227618550-227618551
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227504042..227507688-chr1:227616722..227620233,4	K562	blood:
2	chr1:227505302..227507077-chr1:227617949..227620450,2	MCF-7	breast:
3	chr1:227506036..227507932-chr1:227615818..227619997,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF678-1	chr1:227617106-227618736	ENSG00000234277.2

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10082258	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3000775	0.81[CHB][hapmap]
rs3000778	0.88[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3000779	0.90[ASN][1000 genomes]
rs3000781	0.90[ASN][1000 genomes]
rs3000782	0.88[ASN][1000 genomes]
rs3000783	0.90[ASN][1000 genomes]
rs3000784	0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs3000785	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3000786	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3000788	0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3000789	0.88[CHB][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3000791	0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3000792	0.88[CHB][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3000793	0.83[ASN][1000 genomes]
rs3000794	0.90[ASN][1000 genomes]
rs3000796	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3000797	0.88[CHB][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3000798	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3000804	0.82[CHB][hapmap]
rs3000806	0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3000807	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3000809	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3000810	0.81[CHB][hapmap]
rs3000811	0.84[ASN][1000 genomes]
rs3014277	0.83[ASN][1000 genomes]
rs3014278	0.84[ASN][1000 genomes]
rs3014279	0.86[JPT][hapmap]
rs3014280	0.81[CHB][hapmap]
rs3014287	0.88[CHB][hapmap];0.90[ASN][1000 genomes]
rs3014288	0.90[ASN][1000 genomes]
rs3014290	0.88[CHB][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3014291	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3014292	0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs3014293	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3014295	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3014296	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3014297	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3014298	0.87[CHB][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3014299	0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3014300	0.94[CHB][hapmap];0.84[JPT][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3014301	0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3122560	0.84[ASN][1000 genomes]
rs3122561	0.84[ASN][1000 genomes]
rs3125124	0.84[ASN][1000 genomes]
rs4468130	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4570389	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6702589	0.81[CHB][hapmap]
rs9426519	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9426520	0.85[ASN][1000 genomes]
rs9426521	0.94[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv945335	chr1:227618159-227618832	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227615200-227619400	Enhancers	Brain Hippocampus Middle	brain
2	chr1:227615200-227619600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:227615200-227621000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:227615400-227619400	Enhancers	Brain Anterior Caudate	brain
5	chr1:227615400-227623400	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:227615600-227621000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr1:227616000-227618800	Enhancers	Brain Angular Gyrus	brain
8	chr1:227616000-227619200	Enhancers	Brain Substantia Nigra	brain
9	chr1:227616000-227622200	Enhancers	Fetal Muscle Leg	muscle
10	chr1:227616200-227619400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:227616200-227619800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:227616200-227620000	Enhancers	Fetal Muscle Trunk	muscle
13	chr1:227616400-227618600	Enhancers	Left Ventricle	heart
14	chr1:227616400-227618600	Enhancers	NH-A	brain
15	chr1:227616400-227618800	Enhancers	Placenta	Placenta
16	chr1:227616400-227620000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:227616400-227621000	Enhancers	Lung	lung
18	chr1:227616600-227619400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:227616600-227619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:227616600-227625200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:227616800-227619400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr1:227616800-227619400	Weak transcription	Hela-S3	cervix
23	chr1:227617200-227619400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:227617400-227619200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:227617400-227619200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:227617400-227619600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:227617400-227620800	Weak transcription	Spleen	Spleen
28	chr1:227617400-227625200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:227617600-227618800	Enhancers	HSMM	muscle
30	chr1:227617600-227619000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:227617600-227619200	Weak transcription	Right Ventricle	heart
32	chr1:227617600-227619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:227617600-227619400	Weak transcription	Gastric	stomach
34	chr1:227617600-227619400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:227617600-227619600	Weak transcription	Pancreas	Pancrea
36	chr1:227617600-227621400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:227617600-227624000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:227617600-227624400	Weak transcription	Fetal Lung	lung
39	chr1:227617600-227625200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:227617600-227625200	Weak transcription	Fetal Intestine Small	intestine
41	chr1:227617600-227631200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:227617800-227618600	Enhancers	NHDF-Ad	bronchial
43	chr1:227617800-227618800	Enhancers	Adipose Nuclei	Adipose
44	chr1:227617800-227619200	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:227617800-227619200	Weak transcription	Fetal Brain Male	brain
46	chr1:227617800-227619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:227617800-227619400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:227617800-227619400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:227617800-227625200	Weak transcription	Fetal Kidney	kidney
50	chr1:227617800-227625200	Weak transcription	Psoas Muscle	Psoas

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