Variant report

Variant	rs4671956
Chromosome Location	chr2:54773755-54773756
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54767808..54771330-chr2:54771769..54776449,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSPYL6-3	chr2:54773608-54773814	ENSG00000234943.2

Variant related genes	Relation type
ENSG00000228108	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10165490	0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs10180713	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1047499	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]
rs11885703	0.81[EUR][1000 genomes]
rs11892788	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11898012	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12104998	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12105792	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12468469	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12617036	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713260	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13016942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13399435	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1367295	0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1541854	0.91[EUR][1000 genomes]
rs17344044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17344072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521078	0.95[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1802889	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1864493	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292356	0.86[EUR][1000 genomes]
rs2292357	0.82[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes]
rs2941586	0.86[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2941587	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2941595	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2971877	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]
rs2971879	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2971883	1.00[AFR][1000 genomes]
rs2971887	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs354231	0.84[CEU][hapmap]
rs354236	0.84[TSI][hapmap]
rs3796014	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4233952	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4233954	0.85[EUR][1000 genomes]
rs4444573	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4455199	0.91[EUR][1000 genomes]
rs4514917	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4592889	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671221	0.90[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671222	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671225	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671226	1.00[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4671945	0.95[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671946	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671947	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671949	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671950	0.80[CHB][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4671951	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671953	0.80[EUR][1000 genomes]
rs4671954	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671955	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671960	0.83[TSI][hapmap]
rs4671961	0.84[TSI][hapmap]
rs4990319	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545411	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545413	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545414	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545415	0.91[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545418	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545419	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545420	0.80[EUR][1000 genomes]
rs6545427	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545434	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6704769	0.95[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6706372	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs6724590	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6729826	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731661	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs6732949	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6734658	0.91[EUR][1000 genomes]
rs6735813	0.89[EUR][1000 genomes]
rs6742607	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6746016	0.86[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6746306	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6748816	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6761369	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761398	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7563706	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7589236	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7607451	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs907135	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
rs4671956	EML6	cis	Thyroid	GTEx
rs4671956	SPTBN1	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
3	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
6	chr2:54762000-54775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:54762200-54773800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:54763000-54776000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:54764000-54776800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:54765600-54774000	Weak transcription	Fetal Brain Female	brain
11	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:54768400-54775800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:54769800-54775400	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:54769800-54775600	Weak transcription	Fetal Stomach	stomach
15	chr2:54769800-54777000	Weak transcription	Psoas Muscle	Psoas
16	chr2:54770000-54777400	Weak transcription	GM12878-XiMat	blood
17	chr2:54770400-54775000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:54770400-54775400	Weak transcription	Lung	lung
19	chr2:54770400-54776800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:54770600-54773800	Weak transcription	Colonic Mucosa	Colon
22	chr2:54770600-54775400	Weak transcription	Right Atrium	heart
23	chr2:54770600-54776800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:54770600-54780200	Enhancers	Fetal Intestine Large	intestine
25	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:54772400-54774600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:54772600-54773800	Flanking Active TSS	HepG2	liver
28	chr2:54772600-54773800	Enhancers	NHEK	skin
29	chr2:54772600-54774000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:54772600-54774000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:54772600-54774000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:54772600-54774000	Enhancers	Fetal Heart	heart
33	chr2:54772600-54774000	Enhancers	Stomach Mucosa	stomach
34	chr2:54772600-54774000	Flanking Active TSS	A549	lung
35	chr2:54772600-54774000	Enhancers	HUVEC	blood vessel
36	chr2:54772600-54774000	Enhancers	Osteobl	bone
37	chr2:54772600-54774200	Enhancers	Brain Hippocampus Middle	brain
38	chr2:54772600-54774200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:54772600-54774200	Enhancers	HMEC	breast
40	chr2:54772600-54774200	Enhancers	NHDF-Ad	bronchial
41	chr2:54772600-54774600	Enhancers	Brain Substantia Nigra	brain
42	chr2:54772600-54778800	Enhancers	Brain Anterior Caudate	brain
43	chr2:54772600-54780200	Enhancers	Fetal Intestine Small	intestine
44	chr2:54772800-54773800	Enhancers	Aorta	Aorta
45	chr2:54772800-54773800	Enhancers	Colon Smooth Muscle	Colon
46	chr2:54772800-54773800	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr2:54772800-54773800	Enhancers	Small Intestine	intestine
48	chr2:54772800-54774000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:54772800-54774000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:54772800-54774000	Enhancers	Adipose Nuclei	Adipose

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