Variant report

Variant	rs4444573
Chromosome Location	chr2:54827079-54827080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54785770..54787299-chr2:54826149..54827905,2	K562	blood:
2	chr2:54822696..54824811-chr2:54826177..54828033,3	K562	blood:
3	chr2:54815022..54818519-chr2:54825874..54828742,4	K562	blood:
4	chr2:54822853..54825212-chr2:54825239..54827897,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10165490	1.00[YRI][hapmap]
rs10180713	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1047499	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11885703	0.85[EUR][1000 genomes]
rs11892788	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11898012	0.88[TSI][hapmap];1.00[YRI][hapmap]
rs12104998	0.86[CEU][hapmap];0.90[GIH][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs12105792	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12468469	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617036	0.87[EUR][1000 genomes]
rs12713260	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13016942	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13399435	1.00[YRI][hapmap]
rs1367295	0.86[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs1510611	0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1541854	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs168506	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs171350	0.82[EUR][1000 genomes]
rs17344072	0.82[CEU][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs17521078	0.86[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs1864493	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2048371	0.82[EUR][1000 genomes]
rs2271322	0.85[EUR][1000 genomes]
rs2292356	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2292357	0.90[EUR][1000 genomes]
rs2931463	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2931464	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2941584	0.82[MEX][hapmap]
rs2941586	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2941587	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2941591	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2941595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2971875	0.81[EUR][1000 genomes]
rs2971877	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2971879	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2971883	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2971887	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3106204	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs354213	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs354223	0.82[AMR][1000 genomes]
rs354226	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs354228	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs354231	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs354236	0.86[TSI][hapmap]
rs3796014	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4233952	0.83[EUR][1000 genomes]
rs4455199	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4592889	0.89[EUR][1000 genomes]
rs4671221	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs4671222	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs4671225	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4671226	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4671945	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs4671946	0.87[EUR][1000 genomes]
rs4671947	0.87[EUR][1000 genomes]
rs4671949	0.89[EUR][1000 genomes]
rs4671950	0.86[TSI][hapmap]
rs4671951	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4671955	0.84[EUR][1000 genomes]
rs4671956	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4671960	0.81[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4671961	0.82[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4990319	0.87[EUR][1000 genomes]
rs6545411	0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs6545413	0.81[EUR][1000 genomes]
rs6545414	0.81[EUR][1000 genomes]
rs6545415	0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6545418	0.83[EUR][1000 genomes]
rs6545419	0.82[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6545427	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6545429	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6545434	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6704769	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs6706372	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6724590	0.84[EUR][1000 genomes]
rs6729826	0.82[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs6731661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732949	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6734658	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6735813	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6742607	0.81[EUR][1000 genomes]
rs6746016	1.00[YRI][hapmap]
rs6746306	0.83[EUR][1000 genomes]
rs6748816	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6760298	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6761369	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6761398	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7563706	0.84[EUR][1000 genomes]
rs7589236	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7607451	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs907135	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4444573	EML6	cis	Thyroid	GTEx
rs4444573	SPTBN1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54822200-54827800	Genic enhancers	Fetal Muscle Leg	muscle
5	chr2:54822200-54828800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:54822200-54833800	Genic enhancers	HepG2	liver
7	chr2:54822400-54827600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:54822400-54827800	Enhancers	Colon Smooth Muscle	Colon
9	chr2:54822400-54833600	Enhancers	Psoas Muscle	Psoas
10	chr2:54822400-54833800	Enhancers	Stomach Mucosa	stomach
11	chr2:54822400-54834000	Enhancers	Right Atrium	heart
12	chr2:54822600-54827200	Enhancers	Brain Hippocampus Middle	brain
13	chr2:54822800-54831600	Genic enhancers	A549	lung
14	chr2:54823200-54831000	Genic enhancers	Fetal Intestine Large	intestine
15	chr2:54823400-54827200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:54823800-54829400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:54824000-54829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:54824200-54827400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:54824200-54827400	Weak transcription	Fetal Kidney	kidney
20	chr2:54824200-54829600	Enhancers	Fetal Heart	heart
21	chr2:54824200-54830600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:54824200-54833600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:54824400-54828800	Enhancers	HMEC	breast
24	chr2:54824400-54829200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:54824600-54834400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:54824800-54829600	Genic enhancers	Primary hematopoietic stem cells	blood
27	chr2:54824800-54834400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:54825000-54829200	Genic enhancers	HSMM	muscle
30	chr2:54825000-54829800	Weak transcription	Fetal Brain Male	brain
31	chr2:54825200-54827600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:54825200-54828400	Strong transcription	GM12878-XiMat	blood
33	chr2:54825400-54827600	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr2:54825400-54827600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
35	chr2:54825400-54827800	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr2:54825400-54828200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:54825400-54828800	Strong transcription	Fetal Stomach	stomach
38	chr2:54825400-54829000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:54825600-54827200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr2:54825600-54827200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:54825600-54827200	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr2:54825600-54827600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:54825600-54827600	Genic enhancers	Brain Inferior Temporal Lobe	brain
44	chr2:54825600-54827600	Genic enhancers	Brain Substantia Nigra	brain
45	chr2:54825600-54827600	Enhancers	Esophagus	oesophagus
46	chr2:54825600-54827600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr2:54825600-54827600	Genic enhancers	HUVEC	blood vessel
48	chr2:54825600-54827800	Genic enhancers	Brain Anterior Caudate	brain
49	chr2:54825600-54827800	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr2:54825600-54828400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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