Variant report

Variant	rs2185955
Chromosome Location	chr6:28222980-28222981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28220144..28224072-chr6:28306303..28309254,3	K562	blood:
2	chr6:28219253..28222051-chr6:28222330..28224548,2	K562	blood:
3	chr6:28219546..28223731-chr6:28316147..28319107,5	K562	blood:
4	chr6:28219997..28223882-chr6:28224379..28228192,5	K562	blood:
5	chr6:28219245..28221589-chr6:28221663..28224285,2	K562	blood:

Variant related genes	Relation type
ENSG00000187626	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000189298	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1150717	0.91[EUR][1000 genomes]
rs1150719	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs1150720	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs11751702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756111	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11757730	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11758148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11758337	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11970439	1.00[JPT][hapmap]
rs1474589	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs16893817	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs16893937	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17301128	1.00[JPT][hapmap]
rs1736904	0.86[YRI][hapmap]
rs17776284	1.00[JPT][hapmap]
rs1778477	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1778478	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2235358	1.00[JPT][hapmap]
rs2235359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281043	0.82[GIH][hapmap]
rs2299031	1.00[JPT][hapmap]
rs3800326	1.00[JPT][hapmap]
rs55831267	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6456811	0.82[GIH][hapmap]
rs6903652	1.00[JPT][hapmap]
rs6903823	0.88[JPT][hapmap]
rs6905368	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6912584	0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6921919	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6922111	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs73740584	0.81[AFR][1000 genomes]
rs73740587	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7741443	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7769054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs993619	0.92[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2185955	AL022393.7	cis	Thyroid	GTEx
rs2185955	HIST1H4C	cis	parietal	SCAN
rs2185955	HFE	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28220600-28226600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:28220600-28226600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:28220600-28226600	Weak transcription	HSMM	muscle
4	chr6:28220600-28226600	Weak transcription	NHEK	skin
5	chr6:28220600-28226800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:28220600-28226800	Weak transcription	HSMMtube	muscle
7	chr6:28220600-28226800	Weak transcription	NH-A	brain
8	chr6:28220800-28226400	Weak transcription	Pancreas	Pancrea
9	chr6:28220800-28226400	Weak transcription	Psoas Muscle	Psoas
10	chr6:28220800-28226400	Weak transcription	Right Atrium	heart
11	chr6:28220800-28226600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:28220800-28226600	Weak transcription	HMEC	breast
13	chr6:28220800-28226600	Weak transcription	HUVEC	blood vessel
14	chr6:28220800-28226600	Weak transcription	Osteobl	bone
15	chr6:28220800-28226800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:28220800-28226800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:28220800-28226800	Weak transcription	Lung	lung
18	chr6:28220800-28227000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:28220800-28227000	Weak transcription	Gastric	stomach
20	chr6:28221200-28226400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:28221200-28226600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:28221600-28226600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:28221800-28226600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:28222400-28226400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:28222600-28226400	Weak transcription	Monocytes-CD14+_RO01746	blood

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