Variant report

Variant	rs17676641
Chromosome Location	chr6:12047583-12047584
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:12042974..12045827-chr6:12047311..12049973,3	K562	blood:
2	chr6:12010545..12015080-chr6:12042990..12048217,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095951	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10223323	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62395289	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296246	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9462420	0.92[ASN][1000 genomes]
rs9470838	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470843	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs964432	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885932	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17676641	NEDD9	cis	parietal	SCAN
rs17676641	MAK	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12018600-12049400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:12018600-12052000	Weak transcription	Thymus	Thymus
3	chr6:12023200-12047800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:12032000-12047600	Weak transcription	Fetal Stomach	stomach
5	chr6:12034800-12047600	Weak transcription	Fetal Intestine Large	intestine
6	chr6:12034800-12061000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:12035000-12049800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:12035200-12047800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:12035200-12052200	Weak transcription	Stomach Mucosa	stomach
10	chr6:12038000-12047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:12040200-12047600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:12040200-12048000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:12040200-12048600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:12040200-12060800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:12040400-12049400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:12040400-12050200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:12040400-12058800	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:12040400-12059600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:12041000-12060800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:12041400-12048200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:12041400-12052200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:12042200-12050000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:12044200-12047600	Weak transcription	Fetal Intestine Small	intestine
24	chr6:12045200-12047600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:12045200-12049200	Weak transcription	Fetal Brain Female	brain
26	chr6:12045200-12049400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:12045200-12052000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:12045400-12049400	Weak transcription	HepG2	liver
29	chr6:12045400-12050000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:12045400-12051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:12045400-12052600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:12045600-12047600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:12045600-12047600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:12045600-12047600	Weak transcription	Lung	lung
35	chr6:12045600-12047600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:12045600-12047600	Weak transcription	Spleen	Spleen
37	chr6:12045600-12047600	Weak transcription	K562	blood
38	chr6:12045600-12047800	Weak transcription	Primary B cells from cord blood	blood
39	chr6:12045600-12047800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:12045600-12049000	Weak transcription	NH-A	brain
41	chr6:12045600-12049200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:12045600-12049400	Weak transcription	Ovary	ovary
43	chr6:12045600-12049600	Weak transcription	Adipose Nuclei	Adipose
44	chr6:12045600-12050800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:12045600-12051400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:12045600-12051400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:12045600-12056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:12045600-12058200	Weak transcription	Small Intestine	intestine
49	chr6:12045600-12058600	Weak transcription	A549	lung
50	chr6:12045600-12058800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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