Variant report

Variant	rs229244
Chromosome Location	chr14:31085088-31085089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31074562..31083390-chr14:31084587..31093565,15	K562	blood:
2	chr14:31083098..31087151-chr14:31087433..31093138,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092140	Chromatin interaction
ENSG00000092108	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10131166	0.83[AMR][1000 genomes]
rs10141944	0.83[AMR][1000 genomes]
rs10146357	0.86[CHB][hapmap];0.80[CHD][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs10147257	0.86[CHB][hapmap]
rs10149966	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1123860	0.86[CHB][hapmap]
rs11623154	0.83[AMR][1000 genomes]
rs11626600	0.90[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs11627421	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11628700	0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes]
rs11846408	0.86[CHB][hapmap]
rs11851205	0.83[AMR][1000 genomes]
rs12882048	0.97[ASN][1000 genomes]
rs12882931	0.86[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs12894186	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs170665	0.82[EUR][1000 genomes]
rs17096941	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs17097023	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2045180	0.81[EUR][1000 genomes]
rs2057284	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2070340	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2273520	0.83[AMR][1000 genomes]
rs2273521	0.86[CHB][hapmap];0.83[AMR][1000 genomes]
rs2273522	0.86[CHB][hapmap];0.83[MEX][hapmap]
rs229150	0.85[ASW][hapmap]
rs229175	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs229179	0.82[CHB][hapmap]
rs229184	0.82[CHB][hapmap]
rs229201	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs229231	0.81[EUR][1000 genomes]
rs229236	0.82[EUR][1000 genomes]
rs229237	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[EUR][1000 genomes]
rs229240	0.82[EUR][1000 genomes]
rs229243	0.82[EUR][1000 genomes]
rs2378780	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28567474	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35069045	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs35389182	0.87[ASN][1000 genomes]
rs4430662	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs447853	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs448175	0.81[CHB][hapmap];0.88[CHD][hapmap];0.80[EUR][1000 genomes]
rs58049	0.82[CHB][hapmap]
rs6571356	0.83[AMR][1000 genomes]
rs6571357	0.83[AMR][1000 genomes]
rs7141333	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7141624	0.80[ASN][1000 genomes]
rs7149113	0.83[AMR][1000 genomes]
rs761956	0.86[CHB][hapmap]
rs8006314	0.82[CEU][hapmap]
rs8008094	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8013017	0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs8015536	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs8018993	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8019637	0.83[AMR][1000 genomes]
rs9322864	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs229244	SCFD1	cis	parietal	SCAN
rs229244	SCFD1	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31043000-31090600	Weak transcription	Small Intestine	intestine
2	chr14:31053800-31090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr14:31054200-31090400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr14:31054800-31087200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:31055000-31086800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr14:31055600-31088000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr14:31061600-31090400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr14:31064400-31087800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr14:31064800-31086600	Strong transcription	Dnd41	blood
10	chr14:31064800-31087800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr14:31065600-31086600	Strong transcription	HepG2	liver
12	chr14:31065800-31086800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:31065800-31087000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:31065800-31087600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr14:31069000-31090600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr14:31069000-31090800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr14:31069600-31090400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr14:31070400-31090600	Weak transcription	Spleen	Spleen
19	chr14:31071000-31090600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:31071000-31090600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr14:31071400-31090200	Weak transcription	Fetal Brain Female	brain
22	chr14:31071400-31090400	Weak transcription	Colonic Mucosa	Colon
23	chr14:31071400-31090800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr14:31072200-31090400	Weak transcription	Aorta	Aorta
25	chr14:31072200-31090400	Weak transcription	Colon Smooth Muscle	Colon
26	chr14:31072400-31090600	Weak transcription	Lung	lung
27	chr14:31073800-31090200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr14:31073800-31090200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr14:31073800-31090600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr14:31074400-31090200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr14:31074400-31090400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr14:31074400-31090400	Weak transcription	Fetal Intestine Small	intestine
33	chr14:31074400-31090400	Weak transcription	Fetal Stomach	stomach
34	chr14:31074400-31090600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr14:31074600-31090200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr14:31074800-31090200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr14:31075000-31090200	Weak transcription	Fetal Intestine Large	intestine
38	chr14:31078000-31090400	Weak transcription	Adipose Nuclei	Adipose
39	chr14:31078000-31090400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr14:31078200-31085200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr14:31078200-31090200	Weak transcription	Psoas Muscle	Psoas
42	chr14:31078200-31090200	Weak transcription	Thymus	Thymus
43	chr14:31078200-31090400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr14:31078200-31090400	Weak transcription	Fetal Muscle Leg	muscle
45	chr14:31078400-31090400	Weak transcription	Fetal Kidney	kidney
46	chr14:31078600-31090200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr14:31080000-31090400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr14:31080000-31090600	Weak transcription	Fetal Brain Male	brain
49	chr14:31080200-31090400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr14:31080200-31090400	Weak transcription	Left Ventricle	heart

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