Variant report

Variant	rs229144
Chromosome Location	chr14:31093835-31093836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:31093336-31094045	HepG2	liver:	n/a	n/a
2	POLR2A	chr14:31093343-31093867	GM12878	blood:	n/a	n/a
3	POLR2A	chr14:31093208-31094022	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:31092450..31095408-chr14:31105361..31109368,4	K562	blood:
2	chr14:31090029..31096005-chr14:31342159..31346650,8	K562	blood:
3	chr14:31027121..31031753-chr14:31090278..31094067,6	K562	blood:
4	chr14:31041060..31043251-chr14:31093462..31096063,2	MCF-7	breast:
5	chr14:31039096..31040626-chr14:31092692..31094445,2	MCF-7	breast:
6	chr14:31092450..31095337-chr14:31106738..31109368,2	K562	blood:
7	chr14:31092884..31094625-chr14:31094770..31097263,2	MCF-7	breast:

No data

Variant related genes	Relation type
SCFD1	TF binding region
ENSG00000100473	Chromatin interaction
ENSG00000092108	Chromatin interaction
ENSG00000092140	Chromatin interaction
ENSG00000257636	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10130830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10139154	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10142331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10146357	0.81[CHB][hapmap]
rs10147257	0.82[CHB][hapmap]
rs10147505	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1123860	0.82[CHB][hapmap]
rs11625381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11627421	0.81[CHB][hapmap]
rs11628700	0.81[CHB][hapmap]
rs11846408	0.81[CHB][hapmap]
rs11846420	0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12432098	1.00[YRI][hapmap]
rs12434151	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12882931	0.81[CHB][hapmap]
rs151123	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];1.00[ASN][1000 genomes]
rs170663	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs170665	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17097023	0.80[CHB][hapmap]
rs172946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs179287	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs183467	0.85[EUR][1000 genomes]
rs1950882	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2045180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2070340	0.81[CHB][hapmap]
rs2273521	0.82[CHB][hapmap]
rs2273522	0.80[CHB][hapmap]
rs229141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229143	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229145	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229155	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229156	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229162	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229171	0.85[EUR][1000 genomes]
rs229173	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229176	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229179	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229184	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229190	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs229194	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229195	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229200	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229201	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229206	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs229207	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs229209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229221	0.85[EUR][1000 genomes]
rs229222	0.82[EUR][1000 genomes]
rs229227	0.86[EUR][1000 genomes]
rs229228	0.84[EUR][1000 genomes]
rs229231	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs229235	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229236	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229237	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229240	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229243	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229247	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs230340	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs230343	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs230351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230353	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230356	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230360	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs230364	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2378780	0.81[CHB][hapmap]
rs2378781	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2378782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34558066	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35069045	0.81[CHB][hapmap]
rs35349033	0.82[ASN][1000 genomes]
rs4430662	0.81[CHB][hapmap]
rs448175	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]
rs4981767	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4981770	0.84[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs58049	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61976711	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6571361	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7141161	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7141333	0.82[CHB][hapmap]
rs7142948	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7144204	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7147530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7152417	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7153509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7153747	0.91[CEU][hapmap]
rs7154847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7158351	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs761956	0.82[CHB][hapmap]
rs8006314	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs8008094	0.81[CHB][hapmap]
rs8012494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8013017	0.82[CHB][hapmap]
rs8015536	0.82[CHB][hapmap]
rs9322864	0.81[CHB][hapmap]
rs9806111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs229144	SCFD1	cis	Whole Blood	GTEx
rs229144	SCFD1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31091000-31094000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr14:31092000-31095000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:31092200-31094200	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr14:31092200-31095000	Weak transcription	Left Ventricle	heart
5	chr14:31092200-31095000	Weak transcription	Lung	lung
6	chr14:31092200-31100200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:31092200-31104000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:31092200-31121000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr14:31092200-31133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:31092200-31133200	Weak transcription	Esophagus	oesophagus
11	chr14:31092400-31094000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr14:31092400-31094000	Flanking Active TSS	Dnd41	blood
13	chr14:31092400-31095000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr14:31092400-31095200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr14:31092400-31095400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr14:31092400-31095600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr14:31092400-31096000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr14:31092400-31096200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr14:31092400-31096600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr14:31092400-31099600	Weak transcription	Placenta	Placenta
21	chr14:31092400-31099800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr14:31092400-31100200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr14:31092400-31122800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr14:31092600-31094000	Enhancers	Primary B cells from peripheral blood	blood
25	chr14:31092600-31094200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr14:31092600-31095000	Weak transcription	Colonic Mucosa	Colon
27	chr14:31092600-31095000	Weak transcription	Fetal Muscle Leg	muscle
28	chr14:31092600-31095000	Weak transcription	Fetal Thymus	thymus
29	chr14:31092600-31096200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr14:31092600-31100000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr14:31092800-31094000	Enhancers	Brain Cingulate Gyrus	brain
32	chr14:31092800-31094000	Enhancers	NH-A	brain
33	chr14:31092800-31094200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr14:31092800-31094200	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr14:31092800-31094600	Enhancers	Primary T cells from cord blood	blood
36	chr14:31092800-31094800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr14:31092800-31096000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr14:31092800-31099600	Weak transcription	HSMM	muscle
39	chr14:31092800-31100000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr14:31092800-31102000	Weak transcription	Psoas Muscle	Psoas
41	chr14:31092800-31113200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr14:31092800-31114200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr14:31093000-31094000	Enhancers	HSMMtube	muscle
44	chr14:31093000-31094000	Enhancers	NHEK	skin
45	chr14:31093000-31094200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr14:31093000-31094400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr14:31093000-31098200	Weak transcription	A549	lung
48	chr14:31093200-31094000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr14:31093200-31094000	Genic enhancers	Primary B cells from cord blood	blood
50	chr14:31093200-31094000	Enhancers	Gastric	stomach

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