Variant report

Variant	rs2295709
Chromosome Location	chr6:119231968-119231969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119230333..119232166-chr6:119254664..119256165,2	K562	blood:
2	chr6:119230900..119233116-chr6:119243009..119246627,3	K562	blood:
3	chr6:119230575..119233584-chr6:119242205..119244897,3	MCF-7	breast:
4	chr6:119228532..119230946-chr6:119231114..119234681,5	K562	blood:
5	chr6:119230403..119232175-chr6:119251881..119254660,2	K562	blood:

Variant related genes	Relation type
ENSG00000253194	Chromatin interaction
ENSG00000111877	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10080855	0.81[ASN][1000 genomes]
rs1087453	0.81[ASN][1000 genomes]
rs1087454	0.81[ASN][1000 genomes]
rs11153778	0.86[CEU][hapmap]
rs11153785	0.82[ASN][1000 genomes]
rs11967399	0.83[ASN][1000 genomes]
rs11967889	0.83[ASN][1000 genomes]
rs12191819	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12194515	0.82[ASN][1000 genomes]
rs12196440	0.81[ASN][1000 genomes]
rs12197931	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12200499	0.82[ASN][1000 genomes]
rs12204084	0.86[CEU][hapmap]
rs12206826	0.82[CHB][hapmap]
rs12212179	0.82[ASN][1000 genomes]
rs1321836	0.81[ASN][1000 genomes]
rs1407205	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1407206	0.82[ASN][1000 genomes]
rs17506361	0.86[CEU][hapmap]
rs1762200	0.80[ASN][1000 genomes]
rs2051056	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2051057	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2357020	0.84[ASN][1000 genomes]
rs2357030	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2782575	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs284914	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs284919	0.95[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs2884078	0.82[CHB][hapmap]
rs3798594	0.82[ASN][1000 genomes]
rs3798595	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs3798599	0.82[ASN][1000 genomes]
rs41292550	0.82[ASN][1000 genomes]
rs41292554	0.82[ASN][1000 genomes]
rs415441	0.83[EUR][1000 genomes]
rs4946383	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4946384	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs57100274	0.82[ASN][1000 genomes]
rs57285368	0.83[ASN][1000 genomes]
rs6910327	0.94[JPT][hapmap]
rs6935641	0.82[ASN][1000 genomes]
rs706971	0.82[CHB][hapmap]
rs72966851	0.82[ASN][1000 genomes]
rs72966873	0.81[ASN][1000 genomes]
rs72966896	0.81[ASN][1000 genomes]
rs768995	0.82[ASN][1000 genomes]
rs768996	0.81[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7742473	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7772912	0.86[CEU][hapmap]
rs7775275	0.86[CEU][hapmap]
rs794261	0.80[ASN][1000 genomes]
rs794262	0.88[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs794263	0.80[ASN][1000 genomes]
rs794264	0.80[ASN][1000 genomes]
rs794266	0.80[ASN][1000 genomes]
rs794605	0.83[ASN][1000 genomes]
rs794607	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs794614	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs797017	0.80[CHB][hapmap]
rs811201	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9374757	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9374777	0.82[CHB][hapmap]
rs9387609	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9401101	0.86[CEU][hapmap]
rs9401113	0.83[ASN][1000 genomes]
rs9401118	0.82[CHB][hapmap]
rs9481867	0.82[ASN][1000 genomes]
rs9481868	0.82[ASN][1000 genomes]
rs9481869	0.82[ASN][1000 genomes]
rs9481870	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9481871	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs9481872	0.82[ASN][1000 genomes]
rs9489526	0.94[JPT][hapmap]
rs9489535	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9489536	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9489537	0.82[CHB][hapmap]
rs9489539	0.82[ASN][1000 genomes]
rs9489540	0.82[ASN][1000 genomes]
rs9489541	0.81[ASN][1000 genomes]
rs9489543	0.80[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9489544	0.81[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9489547	0.81[ASN][1000 genomes]
rs962393	0.94[JPT][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	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2295709	MCMDC1	cis	multi-tissue	Pritchard
rs2295709	MCM9	cis	Lymphoblastoid	GTEx
rs2295709	MCM9	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119216600-119233800	Weak transcription	Lung	lung
2	chr6:119216600-119236600	Weak transcription	Gastric	stomach
3	chr6:119216600-119243800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:119216800-119232400	Weak transcription	Colonic Mucosa	Colon
5	chr6:119216800-119232600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:119216800-119233200	Weak transcription	Aorta	Aorta
7	chr6:119216800-119235800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:119217000-119242200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:119217800-119236200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:119218600-119247000	Strong transcription	Fetal Thymus	thymus
11	chr6:119218800-119237200	Strong transcription	Primary hematopoietic stem cells	blood
12	chr6:119219200-119254000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr6:119219200-119254400	Strong transcription	Placenta	Placenta
14	chr6:119219600-119253000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:119219600-119253800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:119220600-119233200	Weak transcription	Pancreas	Pancrea
17	chr6:119220600-119234400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:119220600-119236600	Weak transcription	Esophagus	oesophagus
19	chr6:119220800-119233000	Weak transcription	Fetal Intestine Small	intestine
20	chr6:119220800-119233600	Weak transcription	Right Ventricle	heart
21	chr6:119221200-119255800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:119221400-119246800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:119221600-119236600	Weak transcription	Psoas Muscle	Psoas
24	chr6:119221600-119237400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:119221600-119247800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:119221800-119233800	Weak transcription	Ovary	ovary
27	chr6:119221800-119234400	Strong transcription	K562	blood
28	chr6:119222000-119243200	Strong transcription	HepG2	liver
29	chr6:119222000-119254000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:119222000-119254400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:119222000-119255200	Weak transcription	Fetal Heart	heart
32	chr6:119222200-119237000	Strong transcription	Primary B cells from cord blood	blood
33	chr6:119222200-119245400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:119222200-119253400	Strong transcription	Fetal Intestine Large	intestine
35	chr6:119222400-119246600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr6:119222400-119249600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr6:119222600-119234200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr6:119222600-119251400	Strong transcription	Dnd41	blood
39	chr6:119222600-119253800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:119222600-119253800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:119223600-119235600	Strong transcription	Liver	Liver
42	chr6:119224000-119254000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:119224200-119245600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:119224200-119246000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:119224200-119252800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr6:119224400-119245600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr6:119224600-119233600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr6:119224600-119235800	Strong transcription	Adipose Nuclei	Adipose
49	chr6:119224600-119236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:119224600-119237200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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