Variant report

Variant	rs2105949
Chromosome Location	chr1:174991934-174991935
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr1:174991906-174993178	K562	blood:	n/a	n/a
2	POLR2A	chr1:174991932-174993166	K562	blood:	n/a	n/a
3	POLR2A	chr1:174991542-174993296	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr1:174991823-174993231	IMR90	lung:	n/a	n/a
5	MAZ	chr1:174991789-174993277	IMR90	lung:	n/a	n/a
6	MTA3	chr1:174991820-174993397	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:174991920-174993006	GM12878	blood:	n/a	n/a
8	REST	chr1:174991690-174993277	H1-neurons	neurons:	n/a	n/a
9	GATA1	chr1:174991803-174992908	PBDE	blood:	n/a	n/a
10	RCOR1	chr1:174991917-174993137	K562	blood:	n/a	n/a
11	POLR2A	chr1:174991668-174993294	MCF10A-Er-Src	breast:	n/a	n/a
12	MXI1	chr1:174991886-174993200	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr1:174991841-174993051	IMR90	lung:	n/a	n/a
14	POLR2A	chr1:174991831-174993311	K562	blood:	n/a	n/a
15	POLR2A	chr1:174991924-174993286	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:174991898-174993763	K562	blood:	n/a	n/a
17	HCFC1	chr1:174991537-174993387	Hela-S3	cervix:	n/a	n/a
18	SIN3AK20	chr1:174991927-174993226	MCF-7	breast:	n/a	n/a
19	USF2	chr1:174991808-174993257	Hela-S3	cervix:	n/a	n/a
20	PML	chr1:174991851-174993175	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174982973..174985491-chr1:174991343..174993295,2	MCF-7	breast:
2	chr1:174975701..174977916-chr1:174990172..174992601,2	MCF-7	breast:
3	chr1:174966455..174979047-chr1:174985921..174994239,29	MCF-7	breast:
4	chr1:174967181..174971270-chr1:174989768..174994107,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000206659	TF binding region
ENSG00000120333	Chromatin interaction
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1046439	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912867	1.00[YRI][hapmap]
rs11590474	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs1801791	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1978053	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1984418	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2187562	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2187939	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2285208	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2285210	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301507	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3018410	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap]
rs35996757	0.89[ASN][1000 genomes]
rs3753563	0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap]
rs4651238	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap]
rs6425305	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap]
rs6425309	1.00[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425310	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665216	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap]
rs6669560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7538588	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap]
rs9804056	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947512	chr1:174984818-175000909	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2105949	SLC9A11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174987200-174992000	Weak transcription	Small Intestine	intestine
2	chr1:174987800-174992000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:174987800-174992000	Weak transcription	Spleen	Spleen
4	chr1:174990800-174992000	Flanking Active TSS	Dnd41	blood
5	chr1:174990800-174993000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:174990800-174993200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:174991000-174992000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:174991400-174992000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr1:174991400-174992000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:174991400-174992000	Flanking Active TSS	HUVEC	blood vessel
11	chr1:174991400-174992400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:174991400-174992800	Active TSS	HMEC	breast
13	chr1:174991400-174993000	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:174991400-174993000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:174991400-174993000	Active TSS	A549	lung
16	chr1:174991400-174993000	Active TSS	NHEK	skin
17	chr1:174991400-174993200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr1:174991400-174993200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:174991400-174993200	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:174991400-174993200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:174991400-174993200	Active TSS	Psoas Muscle	Psoas
22	chr1:174991400-174993200	Active TSS	HSMMtube	muscle
23	chr1:174991400-174993200	Active TSS	NHLF	lung
24	chr1:174991600-174992000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:174991600-174992000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:174991600-174992000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:174991600-174992000	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr1:174991600-174992000	Flanking Active TSS	Colon Smooth Muscle	Colon
29	chr1:174991600-174992000	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr1:174991600-174992000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr1:174991600-174992000	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr1:174991600-174992000	Flanking Active TSS	Fetal Thymus	thymus
33	chr1:174991600-174992000	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr1:174991600-174992000	Flanking Active TSS	NH-A	brain
35	chr1:174991600-174992000	Flanking Active TSS	Osteobl	bone
36	chr1:174991600-174992200	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr1:174991600-174992200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:174991600-174992200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr1:174991600-174992200	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:174991600-174992200	Flanking Active TSS	Liver	Liver
41	chr1:174991600-174992200	Flanking Active TSS	Fetal Brain Male	brain
42	chr1:174991600-174992200	Flanking Active TSS	Placenta	Placenta
43	chr1:174991600-174992200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:174991600-174992200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr1:174991600-174992200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr1:174991600-174992400	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr1:174991600-174992400	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr1:174991600-174992800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:174991600-174992800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:174991600-174993000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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