Variant report

Variant	rs448175
Chromosome Location	chr14:31069204-31069205
allele	G/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	chr14:31069143-31069253	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:31062088..31063595-chr14:31068760..31070343,2	MCF-7	breast:
2	chr14:31067708..31069634-chr14:31090291..31092583,3	MCF-7	breast:
3	chr14:31067916..31070610-chr14:31073012..31074923,2	MCF-7	breast:
4	chr14:31069035..31071443-chr14:31073257..31074780,2	K562	blood:
5	chr14:31069000..31071330-chr14:31089606..31092112,2	K562	blood:

Variant related genes	Relation type
G2E3	TF binding region
ENSG00000092140	Chromatin interaction
ENSG00000092108	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10130830	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10139154	0.82[EUR][1000 genomes]
rs10142331	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10147505	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11625381	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11846420	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12432098	1.00[YRI][hapmap]
rs12434151	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12894186	0.81[CHB][hapmap]
rs151123	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs170663	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs170665	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096941	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs172946	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs179287	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs183467	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1950882	0.80[EUR][1000 genomes]
rs2045180	1.00[CEU][hapmap];0.88[CHB][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2070339	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229141	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229143	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229144	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229145	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229150	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229152	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229154	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229155	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229156	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229161	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229162	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229171	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229173	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229176	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229190	0.95[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229194	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229195	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229200	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229206	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229209	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229211	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229221	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs229222	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs229227	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229228	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229231	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs229235	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229236	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229237	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229240	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229243	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229244	0.81[CHB][hapmap];0.88[CHD][hapmap];0.80[EUR][1000 genomes]
rs229247	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230340	0.84[CHB][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap]
rs230351	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs230353	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs230356	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs230360	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs230364	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs230366	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2378781	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2378782	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34558066	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4981767	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4981770	1.00[YRI][hapmap]
rs58049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61976711	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6571361	0.86[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs7141161	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7142948	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7144204	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7147530	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7152417	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7153509	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7153747	0.91[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7154847	0.95[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7158351	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8006314	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs8012494	0.84[CHB][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap]
rs9806111	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[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	nsv564169	chr14:30819087-31541494	Strong transcription Genic enhancers ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1036419	chr14:30969616-31224226	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv901581	chr14:30978745-31585289	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv564171	chr14:31068090-31149630	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs448175	SCFD1	cis	Thyroid	GTEx
rs448175	SCFD1	cis	parietal	SCAN
rs448175	G2E3	cis	parietal	SCAN
rs448175	SCFD1	cis	cerebellum	SCAN
rs448175	SCFD1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31029000-31071800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:31029200-31071800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:31033800-31070000	Weak transcription	Lung	lung
4	chr14:31040200-31069800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:31043000-31079600	Weak transcription	Gastric	stomach
6	chr14:31043000-31090600	Weak transcription	Small Intestine	intestine
7	chr14:31045000-31070000	Weak transcription	Aorta	Aorta
8	chr14:31046800-31069800	Weak transcription	Fetal Kidney	kidney
9	chr14:31047000-31069800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:31047000-31079600	Weak transcription	Pancreas	Pancrea
11	chr14:31049600-31079600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:31050200-31079800	Weak transcription	Brain Angular Gyrus	brain
13	chr14:31051800-31079600	Weak transcription	Fetal Brain Male	brain
14	chr14:31052000-31077400	Weak transcription	Psoas Muscle	Psoas
15	chr14:31053600-31079800	Weak transcription	Brain Substantia Nigra	brain
16	chr14:31053800-31070200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr14:31053800-31090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr14:31054200-31090400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr14:31054800-31072000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr14:31054800-31087200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:31055000-31086800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr14:31055400-31069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:31055400-31070000	Weak transcription	Colonic Mucosa	Colon
24	chr14:31055600-31088000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr14:31057200-31071800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:31057400-31077600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr14:31057800-31079800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr14:31058400-31080000	Weak transcription	Fetal Heart	heart
29	chr14:31058800-31069800	Weak transcription	Spleen	Spleen
30	chr14:31058800-31074800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr14:31059200-31069400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr14:31059600-31069400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr14:31059800-31069400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr14:31059800-31080000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr14:31060000-31070000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr14:31061000-31069400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr14:31061000-31071800	Weak transcription	NHLF	lung
38	chr14:31061400-31070200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr14:31061600-31090400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr14:31063000-31069600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr14:31064200-31078200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr14:31064400-31087800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr14:31064600-31073800	Strong transcription	Primary B cells from cord blood	blood
44	chr14:31064800-31078000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr14:31064800-31086600	Strong transcription	Dnd41	blood
46	chr14:31064800-31087800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr14:31065000-31075000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr14:31065400-31075000	Strong transcription	GM12878-XiMat	blood
49	chr14:31065600-31072600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr14:31065600-31076800	Strong transcription	Primary B cells from peripheral blood	blood

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