Variant report

Variant	rs2281043
Chromosome Location	chr6:28268497-28268498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28265086..28267081-chr6:28267676..28269860,3	K562	blood:
2	chr6:28264442..28268560-chr6:28269964..28273646,5	K562	blood:
3	chr6:28266856..28268560-chr6:28269964..28272119,2	K562	blood:
4	chr6:28255681..28258623-chr6:28265550..28268633,3	K562	blood:
5	chr6:28268157..28273166-chr6:28302896..28306229,5	K562	blood:
6	chr6:28268084..28270649-chr6:28302585..28305878,5	K562	blood:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1062169	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119211	0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1150697	0.80[CEU][hapmap]
rs1150699	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs1150704	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs1150713	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150717	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150720	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752073	0.89[CEU][hapmap]
rs11756111	0.83[GIH][hapmap]
rs1233664	0.80[CEU][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap]
rs1233665	0.80[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs1233666	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs13210258	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1474589	1.00[CEU][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs16893817	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16893937	1.00[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes]
rs16901846	1.00[CEU][hapmap]
rs1736890	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs1736894	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs1778477	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778478	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890809	0.89[CEU][hapmap]
rs2185955	0.82[GIH][hapmap]
rs2232422	1.00[CEU][hapmap]
rs2232428	0.89[CEU][hapmap]
rs2235359	0.83[GIH][hapmap]
rs2622315	0.89[CEU][hapmap]
rs3800325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55831267	0.93[EUR][1000 genomes]
rs56053755	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456811	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];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456814	0.80[ASN][1000 genomes]
rs6905368	0.93[EUR][1000 genomes]
rs6917759	0.89[CEU][hapmap]
rs6923170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929559	0.89[CEU][hapmap]
rs73740584	0.83[ASN][1000 genomes]
rs73742542	0.93[EUR][1000 genomes]
rs7744788	1.00[CEU][hapmap]
rs7769054	0.80[CEU][hapmap]
rs993619	0.80[CEU][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2281043	ZSCAN23	cis	parietal	SCAN
rs2281043	HMGN4	cis	parietal	SCAN
rs2281043	ZSCAN23	cis	cerebellum	SCAN
rs2281043	ZNF323	cis	parietal	SCAN
rs2281043	HIST1H4C	cis	parietal	SCAN
rs2281043	ZNF165	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
2	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28250000-28293800	Weak transcription	Gastric	stomach
4	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
5	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:28250600-28270800	Weak transcription	Fetal Heart	heart
7	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:28250800-28270000	Weak transcription	Psoas Muscle	Psoas
9	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:28251000-28270800	Weak transcription	Colonic Mucosa	Colon
11	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:28255200-28268600	Weak transcription	Ovary	ovary
15	chr6:28255200-28271200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:28255200-28271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
18	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
19	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
21	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:28255400-28271200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:28255400-28278400	Weak transcription	HepG2	liver
24	chr6:28255600-28271400	Weak transcription	Placenta	Placenta
25	chr6:28255600-28272000	Weak transcription	Brain Substantia Nigra	brain
26	chr6:28256400-28271600	Weak transcription	Liver	Liver
27	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:28256600-28268600	Weak transcription	Fetal Thymus	thymus
29	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:28257600-28278800	Weak transcription	NHDF-Ad	bronchial
31	chr6:28257800-28268600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:28257800-28279000	Weak transcription	HMEC	breast
33	chr6:28258000-28268600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:28258000-28268800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:28258000-28270800	Weak transcription	NH-A	brain
36	chr6:28258200-28268600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:28258400-28269600	Weak transcription	Fetal Kidney	kidney
38	chr6:28258400-28273800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr6:28258600-28268600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:28258600-28273000	Weak transcription	Fetal Brain Male	brain
41	chr6:28263200-28270200	Strong transcription	Brain Germinal Matrix	brain
42	chr6:28263400-28269400	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:28264200-28273000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:28264200-28273000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:28264400-28270000	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:28264400-28270200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:28264400-28270400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr6:28264600-28270000	Strong transcription	Adipose Nuclei	Adipose
49	chr6:28264600-28270000	Strong transcription	Fetal Brain Female	brain
50	chr6:28264800-28272000	Weak transcription	HSMM	muscle

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