Variant report

Variant	rs620484
Chromosome Location	chr6:4114211-4114212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4113800..4118980-chr6:4133466..4136327,6	K562	blood:
2	chr6:4112616..4115686-chr6:4134905..4137103,3	MCF-7	breast:
3	chr6:4113998..4116630-chr6:4130932..4132448,2	K562	blood:
4	chr6:4114034..4116069-chr6:4119124..4121517,2	K562	blood:
5	chr6:4112632..4117025-chr6:4117179..4121716,5	K562	blood:
6	chr6:4113549..4115331-chr6:4170875..4173732,2	K562	blood:
7	chr6:4108578..4110178-chr6:4111693..4114473,2	K562	blood:

Variant related genes	Relation type
ENSG00000198721	Chromatin interaction
ENSG00000234817	Chromatin interaction
ENSG00000254821	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs101418	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs11755877	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs1204951	0.92[ASN][1000 genomes]
rs2326408	1.00[ASN][1000 genomes]
rs2473597	0.84[ASN][1000 genomes]
rs2745453	0.84[ASN][1000 genomes]
rs2745455	0.89[ASN][1000 genomes]
rs2783063	0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2783073	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28878015	0.91[ASN][1000 genomes]
rs4959271	0.89[ASN][1000 genomes]
rs582008	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs583782	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs583881	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs584585	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590675	0.84[ASN][1000 genomes]
rs592953	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs593291	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs594662	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs595413	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs608195	0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs609946	0.84[ASN][1000 genomes]
rs611500	1.00[ASN][1000 genomes]
rs612022	0.90[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612477	0.93[ASN][1000 genomes]
rs613028	0.97[ASN][1000 genomes]
rs613260	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613709	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617604	0.90[ASN][1000 genomes]
rs617790	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619439	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs619483	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs619873	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620901	0.83[ASN][1000 genomes]
rs621205	0.90[ASN][1000 genomes]
rs626080	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs627259	0.93[ASN][1000 genomes]
rs629362	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633290	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634114	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs634698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634970	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs638329	0.85[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs639905	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs643232	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646385	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs648900	1.00[ASN][1000 genomes]
rs649725	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651246	0.84[ASN][1000 genomes]
rs653431	0.84[ASN][1000 genomes]
rs654621	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs654982	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs659025	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659051	0.91[ASN][1000 genomes]
rs659305	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597031	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs660560	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660957	0.91[ASN][1000 genomes]
rs661404	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs661657	0.92[ASN][1000 genomes]
rs662834	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs664299	0.98[ASN][1000 genomes]
rs664635	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs664839	0.82[ASN][1000 genomes]
rs664898	0.91[ASN][1000 genomes]
rs665728	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs665894	0.89[ASN][1000 genomes]
rs666254	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs668070	0.88[ASN][1000 genomes]
rs670932	0.84[ASN][1000 genomes]
rs671364	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs674543	0.89[ASN][1000 genomes]
rs676683	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678285	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs679303	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs688176	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs689308	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694058	0.91[ASN][1000 genomes]
rs694903	0.93[ASN][1000 genomes]
rs707991	0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7166	0.91[CEU][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744628	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756630	0.80[ASN][1000 genomes]
rs7757606	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853416	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853418	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9328220	1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378395	0.83[ASN][1000 genomes]
rs9405219	0.90[ASN][1000 genomes]
rs9405701	0.91[ASN][1000 genomes]
rs942475	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs9503919	0.82[YRI][hapmap]
rs9503922	0.86[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs620484	ECI2	cis	Thyroid	GTEx
rs620484	C6orf201	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4103400-4115400	Weak transcription	Fetal Brain Male	brain
2	chr6:4103400-4115600	Weak transcription	Fetal Stomach	stomach
3	chr6:4103400-4115600	Weak transcription	Gastric	stomach
4	chr6:4104600-4115600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:4104600-4115600	Weak transcription	Pancreas	Pancrea
6	chr6:4104800-4115000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:4104800-4115200	Weak transcription	HMEC	breast
8	chr6:4107200-4114800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:4109000-4115600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:4109200-4115600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:4110200-4114600	Weak transcription	Brain Germinal Matrix	brain
12	chr6:4110400-4115400	Weak transcription	Fetal Kidney	kidney
13	chr6:4110400-4115600	Weak transcription	Ovary	ovary
14	chr6:4110400-4118400	Weak transcription	A549	lung
15	chr6:4110400-4124400	Weak transcription	Fetal Heart	heart
16	chr6:4110600-4115400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:4110600-4115400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:4110600-4115600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:4110600-4115600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:4110600-4115600	Weak transcription	Fetal Intestine Large	intestine
21	chr6:4110600-4115600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:4110600-4115800	Weak transcription	Small Intestine	intestine
23	chr6:4110800-4115200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:4110800-4115600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:4110800-4115600	Weak transcription	HUVEC	blood vessel
26	chr6:4111000-4115600	Weak transcription	NHEK	skin
27	chr6:4111000-4134200	Weak transcription	Stomach Mucosa	stomach
28	chr6:4111200-4115600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:4112400-4115200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:4112600-4114400	Weak transcription	Fetal Thymus	thymus
31	chr6:4113000-4115200	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:4113200-4114600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:4113200-4115400	Weak transcription	Fetal Brain Female	brain
34	chr6:4113200-4115400	Weak transcription	GM12878-XiMat	blood
35	chr6:4113200-4115600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:4113200-4115600	Weak transcription	Thymus	Thymus
37	chr6:4113400-4114400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:4113400-4114600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:4113400-4114800	Weak transcription	Primary B cells from cord blood	blood
40	chr6:4113400-4114800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:4113400-4115400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:4113400-4115400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:4113400-4115600	Weak transcription	HSMM	muscle
44	chr6:4113600-4114600	Enhancers	HepG2	liver
45	chr6:4113600-4114800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:4113600-4114800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:4113600-4114800	Enhancers	Osteobl	bone
48	chr6:4113600-4115000	Weak transcription	Dnd41	blood
49	chr6:4113600-4115200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr6:4113600-4115200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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