Variant report

Variant	rs10002443
Chromosome Location	chr4:77953658-77953659
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	NFIC	chr4:77953154-77953747	ECC-1	luminal epithelium:	n/a	chr4:77953446-77953462 chr4:77953446-77953463
2	NFIC	chr4:77953061-77953811	SK-N-SH	brain:	n/a	chr4:77953446-77953462 chr4:77953446-77953463

No.	Distal block	Cell Line	Cell type
1	chr4:77947529..77949938-chr4:77951734..77954656,2	K562	blood:
2	chr4:77952881..77954867-chr4:77957235..77958797,2	K562	blood:
3	chr4:77938334..77942143-chr4:77950747..77953977,4	K562	blood:
4	chr4:77953007..77954866-chr4:77959378..77961755,2	MCF-7	breast:

Variant related genes	Relation type
SEPT11	TF binding region
ENSG00000138758	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10006033	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs10031961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10470896	1.00[ASW][hapmap];0.90[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10856952	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap]
rs11559161	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12186	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1472399	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs16996592	1.00[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]
rs17002332	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002334	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17002336	1.00[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]
rs17002339	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17002346	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279711	0.80[CHB][hapmap];0.85[EUR][1000 genomes]
rs2645668	1.00[GIH][hapmap]
rs2645698	0.86[MEX][hapmap]
rs28541859	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28587298	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28626429	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685589	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4076784	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4076785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4252773	1.00[GIH][hapmap]
rs4252887	0.82[ASN][1000 genomes]
rs4252896	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs4252897	0.82[ASN][1000 genomes]
rs4252913	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4252930	0.83[ASN][1000 genomes]
rs4557282	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs6817626	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs6824360	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667891	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10002443	DDX3Y	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77928200-77960800	Strong transcription	Fetal Intestine Large	intestine
2	chr4:77929400-77961800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:77932200-77962000	Strong transcription	Fetal Brain Female	brain
4	chr4:77934000-77957400	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr4:77935800-77957800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr4:77935800-77960800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:77936000-77957600	Strong transcription	Primary hematopoietic stem cells	blood
8	chr4:77936000-77959200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:77936200-77961800	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:77937400-77981400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:77939800-77960800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:77940000-77956800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:77942800-77961000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:77943200-77954600	Weak transcription	Brain Substantia Nigra	brain
15	chr4:77943800-77969200	Weak transcription	Stomach Mucosa	stomach
16	chr4:77944000-77955800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:77944000-77957600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:77944000-77962800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:77944200-77956200	Strong transcription	HMEC	breast
20	chr4:77944200-77956400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:77944200-77957200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr4:77944200-77961200	Strong transcription	Placenta	Placenta
23	chr4:77944200-77983200	Weak transcription	Small Intestine	intestine
24	chr4:77944400-77954800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:77944400-77956000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:77944400-77956200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:77944400-77956800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:77944400-77957000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:77944400-77957400	Strong transcription	Adipose Nuclei	Adipose
30	chr4:77944400-77957600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:77944400-77959800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:77944400-77960800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:77944400-77965400	Weak transcription	Fetal Heart	heart
34	chr4:77945000-77960000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:77945000-77960200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:77945000-77962600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:77945000-77962800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:77945400-77960800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:77945600-77955800	Strong transcription	NHLF	lung
40	chr4:77945600-77958400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:77945600-77962600	Strong transcription	Fetal Muscle Leg	muscle
42	chr4:77946000-77954200	Weak transcription	Colonic Mucosa	Colon
43	chr4:77946000-77955200	Strong transcription	Fetal Kidney	kidney
44	chr4:77946000-77956200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:77946000-77965000	Weak transcription	Esophagus	oesophagus
46	chr4:77946000-77971800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr4:77947400-77955200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr4:77947800-77954600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:77947800-77955800	Strong transcription	NH-A	brain
50	chr4:77947800-77960800	Strong transcription	GM12878-XiMat	blood

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