Variant report

Variant	rs4236141
Chromosome Location	chr6:56404191-56404192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56402144..56405169-chr6:56405351..56407605,3	MCF-7	breast:
2	chr6:56402109..56404865-chr6:56433971..56436313,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11753813	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11756977	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11758339	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs11759493	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11961668	0.83[ASN][1000 genomes]
rs12174955	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12527139	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13194746	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13204556	0.84[ASN][1000 genomes]
rs13219448	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1359068	0.82[ASN][1000 genomes]
rs1359070	0.82[ASN][1000 genomes]
rs1535610	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1535612	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16887974	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2064591	0.93[EUR][1000 genomes]
rs2273973	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2273974	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2397226	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs34954984	0.84[ASN][1000 genomes]
rs35671304	0.82[ASN][1000 genomes]
rs35926142	0.84[ASN][1000 genomes]
rs4130060	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4143827	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4143828	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4236139	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4236140	0.86[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4236142	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236143	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236144	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4236145	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4283892	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4329120	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4346846	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4454141	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4466244	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4472350	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4473850	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4499917	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4544910	0.82[ASN][1000 genomes]
rs45486696	0.84[ASN][1000 genomes]
rs4712132	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4712133	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715625	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4715626	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715627	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715628	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715629	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4715630	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4715631	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6459161	0.91[CEU][hapmap];0.80[JPT][hapmap]
rs6459163	0.82[ASN][1000 genomes]
rs656988	0.81[CHB][hapmap]
rs6904202	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6906792	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6907917	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913572	0.82[ASN][1000 genomes]
rs6914184	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6919608	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6922770	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6927258	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs6939305	0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs721475	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72877350	0.84[ASN][1000 genomes]
rs7741295	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743011	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7746753	0.82[ASN][1000 genomes]
rs7755361	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7755573	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7758054	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7759875	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7760640	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7760695	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7761281	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7762629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296848	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9296849	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9296850	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349823	0.87[JPT][hapmap]
rs9349825	0.80[ASN][1000 genomes]
rs9349826	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9349828	0.86[JPT][hapmap]
rs9357921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370533	0.95[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs9370534	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9370535	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9382635	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9396213	0.86[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap]
rs9396214	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9396215	0.84[ASN][1000 genomes]
rs9396218	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9396220	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs9464389	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9475709	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9475713	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9475714	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9475716	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1016868	chr6:56376165-56417631	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56341800-56407400	Weak transcription	Spleen	Spleen
2	chr6:56376400-56407200	Weak transcription	Gastric	stomach
3	chr6:56377200-56404200	Weak transcription	K562	blood
4	chr6:56392400-56406200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:56395400-56405200	Weak transcription	Placenta	Placenta
6	chr6:56397000-56405200	Weak transcription	Brain Germinal Matrix	brain
7	chr6:56397200-56406600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:56397400-56405600	Weak transcription	Fetal Brain Female	brain
9	chr6:56398200-56405000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:56400000-56404200	Weak transcription	Stomach Mucosa	stomach
11	chr6:56400000-56404600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr6:56400000-56405400	Weak transcription	Fetal Thymus	thymus
13	chr6:56400200-56404200	Weak transcription	A549	lung
14	chr6:56400200-56404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:56400200-56405200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:56400200-56405800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:56400400-56407000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:56400800-56404600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:56401000-56404600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:56401200-56404200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:56401200-56404200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:56401400-56404400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:56401600-56404200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr6:56401600-56404200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:56401600-56404800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:56401600-56405000	Weak transcription	Colonic Mucosa	Colon
27	chr6:56401600-56408400	Active TSS	Stomach Smooth Muscle	stomach
28	chr6:56401800-56404200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:56401800-56404400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:56401800-56405200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:56401800-56405600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:56402000-56404600	Enhancers	NHEK	skin
33	chr6:56402200-56404400	Enhancers	NHDF-Ad	bronchial
34	chr6:56402400-56404200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:56402400-56404400	Weak transcription	GM12878-XiMat	blood
36	chr6:56402400-56405000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr6:56402400-56405200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:56402600-56404200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:56402600-56404200	Weak transcription	Brain Angular Gyrus	brain
40	chr6:56402600-56404200	Weak transcription	Fetal Intestine Small	intestine
41	chr6:56402600-56404200	Enhancers	HepG2	liver
42	chr6:56402600-56405400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:56402600-56407200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:56402800-56405000	Enhancers	Hela-S3	cervix
45	chr6:56402800-56408000	Active TSS	Colon Smooth Muscle	Colon
46	chr6:56403000-56404200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:56403000-56404200	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:56403000-56404200	Weak transcription	Right Ventricle	heart
49	chr6:56403000-56404200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:56403000-56404400	Weak transcription	Brain Anterior Caudate	brain

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