Variant report

Variant	rs2273606
Chromosome Location	chr6:24405357-24405358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
2	chr6:24282520..24284715-chr6:24405070..24407671,2	MCF-7	breast:
3	chr6:24404630..24407333-chr6:24559685..24561436,2	K562	blood:
4	chr6:24400786..24404823-chr6:24404929..24410869,7	K562	blood:

Variant related genes	Relation type
ENSG00000112293	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000124532	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1054862	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133526	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889240	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889242	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889253	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16901722	1.00[ASW][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs17306130	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298059	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298060	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747772	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818936	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827641	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271775	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271777	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271781	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45448393	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45478094	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45482500	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45574139	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45590133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461006	0.89[EUR][1000 genomes];0.95[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	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2273606	HIST1H4I	cis	parietal	SCAN
rs2273606	MRS2L	Cis_1M	lymphoblastoid	RTeQTL
rs2273606	ZNF184	cis	parietal	SCAN
rs2273606	HIST1H2BA	cis	parietal	SCAN
rs2273606	HIST1H2BG	cis	parietal	SCAN
rs2273606	GPLD1	cis	Esophagus Muscularis	GTEx
rs2273606	MRS2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24401800-24405400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:24402400-24406600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr6:24402600-24405400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:24402600-24405600	Active TSS	GM12878-XiMat	blood
5	chr6:24402800-24405400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:24402800-24405400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:24402800-24405800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:24403000-24405400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:24404000-24405400	Weak transcription	Esophagus	oesophagus
10	chr6:24404000-24406000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
11	chr6:24404000-24406600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:24404000-24408000	Weak transcription	Aorta	Aorta
13	chr6:24404000-24408000	Weak transcription	Lung	lung
14	chr6:24404000-24408000	Weak transcription	Spleen	Spleen
15	chr6:24404000-24408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:24404000-24413000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:24404200-24405400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:24404200-24405400	Weak transcription	Pancreas	Pancrea
19	chr6:24404200-24413000	Weak transcription	Gastric	stomach
20	chr6:24404400-24405400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:24404400-24407600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:24404400-24412000	Weak transcription	Colonic Mucosa	Colon
23	chr6:24404400-24412400	Weak transcription	Fetal Brain Male	brain
24	chr6:24404400-24412800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:24404400-24412800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:24404400-24413000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:24404600-24405400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:24404600-24405400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:24404600-24405400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:24404600-24405400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:24404600-24405400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:24404600-24405400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:24404600-24405400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr6:24404600-24405400	Weak transcription	Brain Anterior Caudate	brain
35	chr6:24404600-24405400	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:24404600-24405400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:24404600-24405400	Enhancers	Duodenum Mucosa	Duodenum
38	chr6:24404600-24405400	Enhancers	Fetal Intestine Small	intestine
39	chr6:24404600-24405400	Weak transcription	Fetal Kidney	kidney
40	chr6:24404600-24405400	Weak transcription	Fetal Lung	lung
41	chr6:24404600-24405400	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:24404600-24405400	Weak transcription	Fetal Stomach	stomach
43	chr6:24404600-24405400	Weak transcription	Fetal Thymus	thymus
44	chr6:24404600-24405400	Weak transcription	Psoas Muscle	Psoas
45	chr6:24404600-24405400	Weak transcription	Right Ventricle	heart
46	chr6:24404600-24405400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:24404600-24405400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:24404600-24405400	Enhancers	Hela-S3	cervix
49	chr6:24404600-24405400	Weak transcription	HSMM	muscle
50	chr6:24404600-24405400	Active TSS	K562	blood

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