Variant report

Variant	rs229184
Chromosome Location	chr14:31039377-31039378
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr14:31038626-31039466	HepG2	liver:	n/a	n/a
2	FOXA1	chr14:31038849-31039408	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:31038087..31039796-chr14:31041679..31043597,2	MCF-7	breast:
2	chr14:31039096..31040626-chr14:31092692..31094445,2	MCF-7	breast:
3	chr14:31035744..31040643-chr14:31041645..31045084,5	K562	blood:
4	chr14:31027395..31030392-chr14:31038600..31040381,2	K562	blood:
5	chr14:31027965..31029888-chr14:31039177..31041559,3	MCF-7	breast:
6	chr14:31039211..31041266-chr14:31071590..31074584,2	K562	blood:
7	chr14:31038615..31040307-chr14:31049881..31051586,2	MCF-7	breast:

No data

Variant related genes	Relation type
G2E3	TF binding region
ENSG00000092140	Chromatin interaction
ENSG00000257636	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10130830	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10139154	0.81[EUR][1000 genomes]
rs10142331	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10147505	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11625381	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11846420	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12432098	1.00[YRI][hapmap]
rs12434151	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12894186	0.83[CHB][hapmap]
rs151123	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs170663	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs170665	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17096941	0.82[CHB][hapmap]
rs172946	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs179287	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs183467	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2045180	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes]
rs2070339	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs229141	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229143	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs229144	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]
rs229145	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229150	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229152	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229154	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229155	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229156	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229161	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229162	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229171	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229173	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229176	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229190	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229194	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229195	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229200	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229206	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229209	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229211	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229221	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229222	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229227	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229228	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229231	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs229235	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs229236	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs229237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs229240	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs229243	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs229244	0.82[CHB][hapmap]
rs229247	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230340	0.85[CHB][hapmap]
rs230351	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs230353	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs230356	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs230360	0.80[AMR][1000 genomes]
rs230364	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs230366	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2378781	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2378782	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs34558066	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs448175	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]
rs4981767	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4981770	1.00[YRI][hapmap]
rs58049	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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61976711	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6571361	0.87[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7141161	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7142948	0.86[EUR][1000 genomes]
rs7144204	0.91[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7147530	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7152417	0.85[EUR][1000 genomes]
rs7153509	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7153747	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7154847	0.95[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes]
rs7158351	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8006314	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap]
rs8012494	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs9806111	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs229184	SCFD1	cis	Thyroid	GTEx
rs229184	SCFD1	cis	Whole Blood	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31029000-31071800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:31029200-31042200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:31029200-31071800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:31029400-31059400	Weak transcription	Left Ventricle	heart
5	chr14:31029400-31060400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr14:31029800-31054000	Weak transcription	Fetal Intestine Large	intestine
7	chr14:31030200-31053200	Weak transcription	Fetal Muscle Leg	muscle
8	chr14:31030400-31041600	Weak transcription	Brain Anterior Caudate	brain
9	chr14:31030400-31042600	Weak transcription	Ovary	ovary
10	chr14:31030400-31042800	Weak transcription	Primary B cells from cord blood	blood
11	chr14:31030400-31044600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr14:31030400-31046600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr14:31030400-31050600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:31030400-31050600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr14:31030400-31056600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr14:31030400-31059200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr14:31030600-31042400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr14:31030600-31046600	Weak transcription	NH-A	brain
19	chr14:31030800-31046600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr14:31031000-31041600	Weak transcription	HUVEC	blood vessel
21	chr14:31031000-31042600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr14:31031000-31052000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr14:31031200-31042000	Weak transcription	NHEK	skin
24	chr14:31032000-31067400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr14:31032200-31042200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr14:31032200-31046600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:31032200-31056400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr14:31032400-31049400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr14:31032400-31067200	Weak transcription	Fetal Stomach	stomach
30	chr14:31032600-31051600	Weak transcription	Fetal Thymus	thymus
31	chr14:31032600-31051800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:31032800-31051600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr14:31032800-31053200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr14:31033600-31046600	Weak transcription	Thymus	Thymus
35	chr14:31033800-31039400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr14:31033800-31046600	Weak transcription	Fetal Intestine Small	intestine
37	chr14:31033800-31070000	Weak transcription	Lung	lung
38	chr14:31034000-31039800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr14:31034000-31040800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr14:31034000-31040800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr14:31034000-31043600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr14:31034000-31059200	Weak transcription	Fetal Lung	lung
43	chr14:31034200-31042400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr14:31034400-31051800	Weak transcription	HSMM	muscle
45	chr14:31035200-31042600	Weak transcription	Psoas Muscle	Psoas
46	chr14:31035200-31045400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr14:31035600-31054400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr14:31036800-31039400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr14:31037000-31039400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr14:31038000-31040600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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