Variant report

Variant	rs2971877
Chromosome Location	chr2:54889136-54889137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54888467-54889467	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:54889058-54889281	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54790164..54792599-chr2:54886849..54889331,2	K562	blood:
2	chr2:54887215..54889644-chr2:55458708..55461317,2	MCF-7	breast:

Variant related genes	Relation type
SPTBN1	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10165490	1.00[YRI][hapmap]
rs10180713	0.95[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1047499	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11885703	0.82[EUR][1000 genomes]
rs11892788	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11898012	0.83[TSI][hapmap];1.00[YRI][hapmap]
rs12104998	0.81[CEU][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs12105792	1.00[ASW][hapmap];0.81[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12468469	0.91[EUR][1000 genomes]
rs12617036	0.82[EUR][1000 genomes]
rs12624153	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs12713260	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13016942	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13399435	1.00[YRI][hapmap]
rs1367295	0.81[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1541854	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs168506	0.83[EUR][1000 genomes]
rs171350	0.83[EUR][1000 genomes]
rs17344072	0.86[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs17521078	0.81[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs1864493	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2048371	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2271322	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2292356	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2292357	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2931463	0.87[EUR][1000 genomes]
rs2931464	0.87[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2941584	0.85[MEX][hapmap]
rs2941586	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2941587	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2941591	0.88[EUR][1000 genomes]
rs2941595	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];0.86[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];0.96[EUR][1000 genomes]
rs2971875	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2971879	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2971883	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2971887	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3106204	0.85[EUR][1000 genomes]
rs354213	0.85[EUR][1000 genomes]
rs354226	0.82[EUR][1000 genomes]
rs354228	0.86[EUR][1000 genomes]
rs354231	1.00[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs354236	0.81[TSI][hapmap]
rs3796014	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4444573	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4455199	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4592889	0.83[EUR][1000 genomes]
rs4671221	0.90[GIH][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs4671222	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4671225	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4671226	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4671945	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs4671946	0.82[EUR][1000 genomes]
rs4671947	0.82[EUR][1000 genomes]
rs4671949	0.84[EUR][1000 genomes]
rs4671950	0.80[TSI][hapmap]
rs4671951	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4671955	0.81[EUR][1000 genomes]
rs4671956	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4671960	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap]
rs4671961	0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs4990319	0.82[EUR][1000 genomes]
rs6545411	0.89[TSI][hapmap]
rs6545415	0.86[TSI][hapmap]
rs6545419	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs6545427	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6545429	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6545434	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6704769	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs6706372	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6729826	0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6731661	0.95[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6732949	0.95[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6734658	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6735813	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6746016	1.00[YRI][hapmap]
rs6748816	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6761369	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6761398	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7589236	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7607451	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs907135	0.95[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2971877	EML6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54842600-54892000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54846400-54895600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:54846400-54896600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:54846600-54898000	Strong transcription	Dnd41	blood
8	chr2:54846800-54895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:54848600-54892400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:54861800-54898600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:54862200-54896600	Strong transcription	Primary hematopoietic stem cells	blood
12	chr2:54862400-54892800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:54862600-54892400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:54862600-54892400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:54862600-54893400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:54862600-54898400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr2:54863000-54892000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:54863000-54892200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:54863000-54892400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:54863000-54895000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr2:54863000-54898600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:54863000-54899400	Strong transcription	Primary T cells from cord blood	blood
23	chr2:54863600-54897000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:54863800-54897400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:54863800-54898600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:54864200-54893600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr2:54865400-54892800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:54865400-54898400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:54865800-54898200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:54866000-54892800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:54866400-54892400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr2:54866400-54897200	Strong transcription	Primary B cells from cord blood	blood
33	chr2:54867200-54892200	Strong transcription	HSMMtube	muscle
34	chr2:54867200-54892400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:54867200-54892400	Strong transcription	NHEK	skin
36	chr2:54867200-54892800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:54867200-54892800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:54867200-54897800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:54867200-54898200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr2:54868400-54892400	Strong transcription	Fetal Intestine Large	intestine
41	chr2:54868800-54898600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:54869000-54892000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:54869000-54896400	Strong transcription	Colonic Mucosa	Colon
44	chr2:54869400-54892000	Strong transcription	Fetal Lung	lung
45	chr2:54869600-54893400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:54869600-54898600	Strong transcription	Fetal Thymus	thymus
47	chr2:54869800-54890200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:54869800-54891400	Strong transcription	Placenta	Placenta
49	chr2:54869800-54891800	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr2:54869800-54895200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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